Absolutely! We intentionally went with fewer "builder" upgrades for this specific reason. We did some pricing on our own after a couple of options seemed unusually high. Between the builder pushing them and the nitwit site agent for their realty trying to talk us into everything under the sun, we said "no thanks." We'll take the basic items on some stuff and upgrade later at our convenience and at a significantly lower cost. Site agent wants more commission, builder wants a bigger share for work he won't actually be doing himself... In the end it's all done by subcontractors who you could have do the work independently and save a ton of money (we've already used some of the builder's subs for things).
Not that I disagree, but here are a few points to consider.
First off, in any housing upgrade situation, you don't want to customize your home beyond the value of comparable sized homes in your locale. Whether the market is red hot or stale, the appraiser is going to find similar sized homes that moved recently and if you're expecting a sales price above that, you've put yourself in tough situation and may have priced the value beyond what VA or other mortgage companies will finance. Just because you can (upgrade) doesn't always mean you should.
When in situation of getting into a new build and being able to make choices on appliances, flooring, etc., it is wise to compare what the builder is going to charge, but make sure you realize that you are financing those options and it isn't an apples to apples comparison. Look at what each dollar you're going to invest in monthly payments cost you per $1000 versus what the total value of the home will be. In a military market, moving into new build situations is risky because unless you're last home available, the next round of new buyers won't want your custom house when they can opportunity to do what you did with a new home and likely get help with closing costs from a motivated builder. You cannot hope to compete in that situation...and like MB attests, what makes sense for you may be a turn-off for potential buyers.
If you know you're moving in a few years and can reasonably assess strength of market for a few years hence (NOBODY has a crystal ball for that so there is an inherent risk regardless of past trends), it may be better for your cash flow to use opportunity to finance your upgrades in the mortagage vice out of your pocket. Say cost to you is $7 per 1,000 financed and you go for $20,000 of upgrades. That would equate to boosting your mortgage payment $140 a month, but wait....out of that $140, you're getting opportunity to write off a percentage on your taxes. If you are dual income, or in tax bracket that outs you in ~ 20+% of your adjusted gross, that equates to only paying for 80 cents on a dollar when it's all said and done so it's really an expense of $112 per month until you sell the house (note: as long as the market is stable or increasing in value). Adjust that up or down depending on your final tax bracket calculation. So if your upgrades are at that number ($112/month for likely no more than 3 years), you're only tapping your monthly cash flow for roughly $4000 spread evenly over that time span and you had benefit of $20,000 of upgrades from the start. It doesn't matter if you are Bob Villa, Jr and have seen every HGTV show so labor isn't in your calculation, the cost of materials alone are going to tap your monthly cash flow and you should not be considering (other) financing or tapping your savings/ready cash either. So even if you want to do tile or countertops yourself, do you have that much extra cashflow monthly to do $10,000 (assuming your cost is materials alone) worth of upgrades even spread over, say, 12 months? And, if you do, is there something else you want to do with it (ie upgrading your wheels)? And remember, it is difficult to recoup cost of additions and/or upgrades to your home as any realtor will tell you.
Some upgrades improve attractiveness to buyers so they are good bets, others only give you satisfaction of having a customized home so you may end up paying a penalty so-to-speak. A priority should be curbside appeal since most potential buyers (or renters for that matter) get hooked as they pull up to an attractive home. What's inside seals the deal they're already predisposed to make. You can't hardly go wrong with doing landscaping yourself especially low maintenance type efforts that you do yourself and shop smartly for attractive plants and trees. A lot of buyers aren't the do-it-yourself types so they don't want to see the potential of a home inside or out (unless they're looking for a steal, which is counter to your objectives), they want a turn-key situation that they can impress frineds and enjoy. HGTV has lots of great ideas for quick fixes and low cost upgrades for exterior and interiors so watching and heeding their advice is a smart move.
I'll throw out a third option for those who are handy with tools. Find an undervalued home in an established neighborhood that isn't getting much attention from the owners or buyers and get in cheap. Don't do too much that will put you above market for nicest homes in neighborhood, but get after the lanscaping and simpler interior upgrades. Your neighbors will appreciate the transformation and when it comes time to sell, you'll have no problem finding a buyer wanting to take advantage of the sum of your efforts. You still have a cashflow challenge/decision to make, but a second mortgage is an option with prevailing low interest rates IF you don't overstep the loan to value ratio (the mortgage companies wouldn't let you anyway). It's like the
Flip this House episodes on HGTV only you're living in the house. This strategy works extremely well in an increasing warm to hot market. A cold market does offer opportunity to get in cheap, but unless it improves, you're only setting yourself up to owe more than you can sell the house for when it comes time to move. Renting it is an option at that point and your upgrades can make a difference in a cold renter's market. Last thing you want is to get into renting out your home after you depart area and have it sit unrented especially between tenants as your cashflow will really be impacted.
Good luck in whatever you decide to do. Remember that the temptation to improve your nest has to make sense for rolling out of the house when your tour ends. If you can wrangle shore duty close to your sea duty and back to sea duty in same locale, you're in best situation to get some return on investment, but you can't count on that happening.