>> I posted a patch to bug#49931 that adds a new user option.
>> Maybe it could be enabled by default?
>
> Skimming the patch, I think that might make sense.  But perhaps push it
> disabled first, and then we can gain some experience with it, and then
> enable it by default if there's no unforeseen side effects?

Yep, this would be the best course of action.

The new variable completion-use-base-affixes will be also enabled
for the M-up/down feature.  Here is an updated patch that also requires
other two patches from bug#47417 (merged with bug#49931) and bug#48356: