As Tinindian states, the issue becomes when you sell it. Too many threads here about people taking Squiers or parts basses and putting counterfeit "Fender" stickers on them, not to mention the almost daily "is this bass authentic" threads.
My three suggestions:
1. Don't put a Fender sticker on a non-Fender neck ("licensed by Fender" is not Fender).
2. If you modded the bass in any way, in a sale, disclose what you did.
3. When in doubt, keep the original parts, so you can sell it stock (you'll probably get more money, even if the changes were improvements).
While I generally agree with you, it is still quite curious how the company who now owns the name Fender is only too happy to claim the fame for parts basses assembled from bits built by the original Fender company. Point in case being for example Clapton's Blackie or SRV's No.1... Just saying.