Minor point of correction:  Libre Relay is a thing that eliminates almost all the relay restrictions (I think it only keeps the forward compatibility rules that reduce the risk of consensus changes causing forks, and some anti-DOS attack stuff).  The example I think you want is knots.

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If someone wants to filter nonsense from their node, why take that option away?

The proposal that removes the option has been dropped for now, but to answer the question: Because it doesn't actually filter the nonsense from their nodes so long as miners are mining it-- they'll be forced to take it once its mined to stay in consensus.  So it just doesn't work.  And why preserve an option that doesn't even work?  Because every option means more code to maintain, combinatoric blow up in testing complexity (as every combination of settings ought to be tested), users wasting their time figuring out how they should or shouldn't set it,  -- and in this case some collateral harm for the little the setting actually does (e.g. slowing block propagation).

The software is inherently opinionated.  It's authors are trying to publish what is in their view the best way to make something the works, if they weren't the could just give you a copy of GCC and tell you to have fun.   In some cases different users have different needs (like maybe you don't have enough bandwidth to relay transactions and want to be blocks only)  or in some cases the best decision may be unclear or might rapidly change... so in those cases options are well justified.  In this case it doesn't seem so (e.g. there have now been a couple years of people screaming at miners to stop bypassing standardness rules and yet the practice seems to be increasing),  but also there is no particular reason to rush removing it.   If it turned out there was some bad effect of the change, it could be reversed and keeping the knob around for now makes that a little faster and easier.  But at least as far as is known now, other than appeasing apparently confused opinions and precaution there doesn't seem to be much reason to keep it.

Minor point of correction:  Libre Relay is a thing that eliminates almost all the relay restrictions (I think it only keeps the forward compatibility rules that reduce the risk of consensus changes causing forks, and some anti-DOS attack stuff).  The example I think you want is knots.