When you buy a new car, you get to choose from a number of amenities, usually divided into trim packages or options. These packages can make upgrading a car's basic model more cost-effective, but they can also leave you with options you don't like, too. You can always have the dealer install certain options once you buy the car, but that comes with its own set of issues. If you want to make the best decision regarding whether or not to get another trim option, take a look at the immediate and long-term effects each option will have on your driving experience.
Cost is likely your most immediate concern. Upgrading to another trim level will increase the total cost of buying the car, but upgrading by having the dealership retrofit the car bit by bit could be even more expensive. If you plan to get most of the items in the package anyway, then the package is a good buy.
If you're planning to get only a couple of the items (for example, you want a rear window defroster, but it's available only if you get a trim package that contains several other things you don't care about), then you may want to ask about retrofitting prices. You can take the car to the dealer's service center to have it done (that's likely the smartest move as it shouldn't void your car's warranty to have the work done there) or to an independent body shop.
Another issue is how quickly you need the car. Cars with the various trim packages installed are usually available same day or within a couple of days from the dealership. A retrofitted option could take a couple of weeks for all the parts to come in and for there to be an open appointment time. At the same time, if the model with the trim package is on back order and won't be available for a while, then retrofitting could be better because at least you could have the car while you wait for the parts to come in.
More options means more that can break and need maintenance. If you want to reduce the costs of owning the car over time, retrofitting for a couple of options may be better than getting a whole trim package upgrade.
You need to talk to the dealership and service center to find out about costs and timelines. Don't feel rushed, even if you need to get the car in a hurry -- your decision will benefit from careful consideration.