This is pretty much what I did,10 years ago, when I built my 29er.
I test-ride the top model of the Trek Marlin, and loved the way that it rode, but didn’t fancy having to get used to SRAM shifters, as I have Shimano on all of my bikes.
So, I bought the lowest spec model (same frame, lower spec components) and installed better brakes, drivetrain and fork (for about £100 less than the top model)
The fork was a 51mm offset boat anchor (that stopped my shed being blown away, in storm Eunice) and was replaced by a 42mm offset Manitou Tower Pro model.
It’s been absolutely fine, for all these years.
To be fair, I only did that one test ride with 51mm, so can’t really say that I can compare the two.
Still a great bike, though.