Let's consider why you would want to draw by agreement. Draw by agreement implies that neither player believes they can win, which is likely because the game is in a state of relative parity of strength. Fifty-move rule, threefold repetition, and Ko rule are rules intended to prevent endless games. They check to make sure progress is constantly being made. If progress is not being made, it is because players are in a state of relative parity and cannot create an advantage (there is the side possibility of one player being utterly inept that I think should be ignored for the sake of policy). If your issue is that stall vs stall matchups create endless games, then I would think we should prevent endless games from happening. The solution should not be to have a bandage at the ready for
when an endless game is created.
The solution should be to not allow the endless battle to be created at all. For any reason that draw by agreement can be useful, a proper draw condition would suffice.
Logically, draw by agreement is always redundant if there are natural draw conditions. If it is possible to draw such that players see it and want to draw by agreement, then the path the the draw is necessarily either trivial or nontrivial. If it is trivial, then it should not be of consequence for players to complete the path to a draw. If it is nontrivial, then skill is a factor; skill is a valued win condition in every competitive game I can think of. As a result, allowing a draw would be premature. In all situations where draw by agreement is viable, a properly codified draw condition would have prevented the issue as well. We may not "lose" anything from draw by agreement (the next paragraph is where I disagree with this completely unsupported premise simply assumed to be true for some reason), but it certainly doesn't make sense to implement over a real draw condition.
For those unfamiliar with recent (relatively at least) chess history, draw by agreement has actually caused a lot of problems, contrary to what you may be led to believe. All you really need to do is look up "grandmaster draws" and see the problems that draw by agreement have resulted in. Players that are apathetic or wish to act with cartel-like intentions draw by agreement, and this is historically supported. I'm not part of the Smogon tournament community, but I personally would not like to be part of tournaments that all but encourage players that are utterly apathetic to winning and intentionally lose or draw games or act maliciously with some to gain unnatural advantages over others. Yes, players can take advantage of fifty-move rule to do those things intentionally. That should be persecuted as with all those attempting to game the system, not apathetically ignored like this:
If people are really going to mindlessly switch for a couple hunfred turns and then sit there for 30 minutes - 1h just to draw their friend, and that's assuming they're playing someone who wants to draw as much as them, then sure let them do that.
Just as a supporting example, Magic: the Gathering allows for intentional draw (I believe their arbiters can refuse to uphold an intentional draw). Draw by agreement has long posed its own problems in their tournaments as well. If you're unsure or don't know 100% whether or not draw by agreement can be harmful, please do look into chess or MtG for historically supported evidence that show that it can. I struggle to understand why one would fight so hard to preserve this form of endless battle in such a fashion when others here have worked just as hard to stamp out all other forms of it.