All highly biased samples towards using them.
I don't use multiclassing. I use feats but remove a couple.
It wouldn't bother me a bit to join a game which didn't use either. I might even prefer it.
Feats are better than no feats but where the balance really gets out of hand is when rolling for stats is done and tailored magic items. Then feats become very powerful.
So I don't really think CR needs to take it into account. I think if DMs use optional rules they should be expected to be able to gauge what effect on the game they have.
I don't disagree that DMs can be expected to do some heavy lifting (in encounter design and judgment) when they use optional rules, but:
1. I guess we disagree on just how optional some rules are (which is fine - disagreement is what this board is about - as long as it's civil);
2. Aside from that - there is clearly room for a more robust more encompassing CR system if it can provide more accurate results - even if it's a bit more complicated. The DMG has all sorts of optional rules, why not a more robust CR system? Failing that, there is certainly room/likely demand for a 3rd party to do it. There is HUGE demand for good 5e content that adds complexity/robustness to the system. I mean Level Up does exactly that and it's already at nearly 10 fold it's funding goal after day 5!