It depends whether the disabled features break the rules of the App Store, or are fraudulent. Presumably you aren’t doing that.

It is partly an intent issue. If you are attempting to pull one over on Apple by hiding app behavior during review, well, they are not going to be happy about that.

Other folks are also noting that, because humans are sometimes bad at evaluating each others' intent, it is probably a good idea to attempt to make one's intent clear if going this route, lest you annoy the gatekeeper.

Right, but you don't know that they're not rejecting it because of your features being disabled. You only now that they didn't reject it.