Some sage like advise in the previous comments.
I can't really comment on the base vs S argument, I love all Ducati's, they are all special and I do enjoy the mods that others do. Get what you can afford, available at the time and avoid loans 'n' debts. The best and first mod to do on a bike is to own it - outright. I view bikes as a reward for hard work, as an indulgent toy and never a prudent financial investment. Bikes are fun and can certainly be a lot of fun in terms of time and recreation, be it street, track or in the garage - another outlet to decompress.
It is never wise to spend money you have not previously earned nor is it wise to spend on indulgences when it could be spent on necessities. If you don't fall into that trap and thus in the pocket of others then depreciation or resale value will not really be a factor. The only factor becomes what is possible and obtainable.
If you are concerned about depreciation then best not to buy a bike or depend on it holding any form of value, other than the value and experiences you personally have with your bike and too some them experiences can be priceless in their own right. If you mod it, then keep the original parts and as several others have said you can always return the bike to stock and part out the mods to claw back some cash.
I have a couple of friends who were real high flying financial banking types, they amassed a lot of cash and could put their finger through the bridge of their nose if you know what I mean. They were not really happy. They packed it all in and opened a small shop in SF where they both wrench any and all bikes that comes their way. Their happy souls with a lot more friends.
As a wise man once said to me if it flys, floats or ..... rent it as it will end up cheaper .. I don't think I have heeded that advise

well at least ride or drive was not in there.