A few people in the other thread assumed that it was required to fork the code to disable those filters. That’s not the case, the filters can be configured, and are off by default.
To hide the reputation system, here’s a line of CSS that admins can add in the admin area to hide it for every user
That CSS line can also be used by any user wanting to hide the score at the user level.
To be clear, defederation has nothing whatsoever to do with PieFed.
Defederation happens on Lemmy, Mastodon, Friendica, Pixelfed, nodeBB, and every other type of software across the entire Fediverse. It is even an absolutely crucial tool to prevent CSAM which depending on the locality of the affected instance could get it shut down and potentially the instance owner exposed to actual criminal charges. (There are other ways, but typically defederation is the easiest.)
Likewise, lemmy.ml famously censors what they consider cusswords on their instance - with a hard-coded list even, iirc, at least it was at one time, years ago - but then after much outcry this censorship was made optional in the code.
So defederation is a reason to not join an instance in favor of some other one, but has nothing to do with wanting to either avoid or preferentially pick an instance running PieFed. In fact the opposite is true, as the PieFed software allows additional options beyond simply federate vs. defederate, allowing instance admins choices between those two extremes. This finer granularity is so helpful! e.g. the PieFed.zip instance blocks Hexbear.net by default for new users, but explains how to remove that, thereby offering hexbear as opt-in content, rather than having to choose between treating it identically the same as all other instances or else cutting it out entirely.
PieFed also allows notes to be placed onto content, which is particularly helpful for places such as Beehaw where their stated ToS differs from the usual across the rest of the Threadiverse.
In fact I am not aware of any particular reason to avoid running PieFed, but anyway even presuming that such exists, defederation is definitely not among them.
The injection of the developers biases into the software, the misleading error messages, and the block behavior behaving like a shadow ban are more than enough reasons to not touch the software.