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Since the PEP 620 is still a draft, I created PR 21390 to fix the performance issue.
As I wrote, I didn't expect any impact on performances since I added _PyType_HasFeature() which access directly the structure member. But I was wrong. 
This change is not strictly required by my work for now, so I just revert it until the PEP is accepted.
If I reapply the change later, I will take care of ensuring that it's properly optimized in CPython internals (access the member, don't call a function), especially on macOS.
If you want to continue the discussion, please discuss on bpo-40170, since this issue is unrelated.
Stefan Krah:
> This one I have some trouble with. It cites PyPy as a bottleneck,
> but IIRC Armin Rigo was on record saying that such changes would
> not help PyPy, and he would come up with a counter proposal.
> Has this changed?
Raymond:
> Victor, is there any reason PyType_GetFlags() can't be converted to a macro or an inlined function?
Serhiy Storchaka:
> I do not know the purpose of this issue. The new code does not look cleaner to me, but maybe it is only for me.
I explained the rationale in bpo-40170 and PEP 620.
It's not a "cleanup change". Serhiy: we are discussing the commit 45ec5b99aefa54552947049086e87ec01bc2fc9a of bpo-40170.
This discussion is happening in the wrong bpo which seems to confuse people. So I close again this issue which is fixed.