Well, you're probably right about whether people notice, but he's ultimately doing this gig for God, not for ohters. And he wants to do the best he can for that gig. But, I'd agree that letting it go is a good idea. The idea to me is to make the performance you're doing sound the best it can, not to reproduce someone else's worship experience. You're playing in a group that's most likely MUCH different from the group that recorded whichever version of the song you're using as your framework. Different instruments, different people, etc. And the bass' function is to lock the drums with the rest of the music and to define the harmony. That means it's about playing with the folks you're playing with, not some imaginary studio cats.
Do what it takes to make the music sound right with the gear and the people you have to work with.
jte