There's no "fix" because this is not a bug; it's the intended behavior.
I understand that. My own use of the word "fix" was mainly responding to the OP's use of the word in reference to the undesired behaviour. Either way though, it's a figure of speech; if someone perceives the behaviour as undesirable, despite it being intended, then their perception will probably also be that the behaviour has been "fixed".
EDIT - heh, I'm sure there will be people who consider SLX "broken" now that direct drop and solid sides are back 
But yeah, WillLem's fix is not a fix but rather a toggable removal that does not fix the core Issue (replay-mode not being recognisable enough)
There are plans to display the animated "R" graphics on screen (like in WinLemm and SuperLemmini) so I'm pretty sure this will make it clear enough what's going on; I can already draw stuff to the screen, I just need to figure out how to to it at specific times, and for specific durations. It's on its way, though.
A popup the first time it happens could also be a good idea, but - as has been said - more discussion is needed around those kind of specifics.
By simply turning it off from the start a user would never experience the upsides of having it assisting you!
This is intentional, since SuperLemmix is about presenting the game in a more traditional fashion without losing any of the modern advantages - it's in response to those people who have complained about NeoLemmix's entering Replay mode automatically. Even if you know how to cancel it, it can still sometimes be undesirable. i get your point though, anyone that doesn't venture into the settings menu might miss the fact that the feature exists at all, but that's true of any setting that isn't activated by default.
Even worse:
It literally isn't worse. Making any highly visible/gameplay-affecting behaviour optional is nearly always preferable. With that said, if an agreement can be reached on how best to handle "enter auto-Replay mode even when player doesn't have any reason to expect it", then I'll likely revert to having the option on by default.
Either way, it's not a problem. I'm more than happy to respond to feedback in order to make SuperLemmix as good as it can be.