The primary purpose of adding 127.0.0.53 to resolv.conf is for client software that wants to do DNS resolution by itself instead of using NSS -- most notable example is Google Chrome, and third-party software which is statically linked (e. g. Go).
However, other software like NetworkManager or isc-dhcp also calls resolvconf and adds name servers picked up by them -- as they don't talk to resolved directly, resolved reads their DNS servers *from* resolv.conf.
But, software which does its own DNS lookups like the above have to do their own DNSSEC validation too -- you can't both chose to *not* use NSS *and* rely on NSS to do DNSSEC for you..
So, this is indeed a wart, but not easily fixed, and also not that important IMHO. Not using NSS is already broken to some degree, as you also ignore things like nss-{winbind,docker,ldap} etc.
This is so freaking lame :(
[1] Launchpad bug 1624320
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