IMO, a R or SPS will always be more desirable and will always retain / gain value. Appreciate your not looking as an investment but always nice to know your money is “well spent”. To me the 998FE was more of a marketing ploy to use up / end the line of the 998 model, still a great bike though The R and SPS were homologation specials so built for a reason. If your budget can stretch go for the R, they are pretty rare nowadays, a SPS would be a great alternative though.
Welcome and good luck, question - if you want an investment you will possibly not enjoy riding it thinking every mile is losing you money, also SP, SPS, R versions will cost more to maintain if used. Perhaps a clean standard bike for a lot less money would make you just as happy - there's a nice 916 in the Ebay bikes for sale just now you might consider?
There’s a 998 FE just popped up on eBay today only done 691 miles ! £19500 Ono, strong money though That would definitely be a bike if you was to ride the value would be going down instead of up. Your in “R” money for that