Note that there's the "Misc.SaveChannelMuteStatus" hidden setting that you can disable so that the mute status is no longer saved in IT / MPTM / S3M.

I can't think of any songs that use that to do anything special

It's easy to dismiss almost every compatibility setting that way. However, each and everyone of them exists because a song out there would sound wrong if the setting was not present.

As outlined in this forum post, what I would like to have eventually is the possibility to distinguish between muted and disabled channels in OpenMPT; muted channels would still be processed (like in IT), while disabled channels would not be procesessed at all (like in Scream Tracker 3 and a few other trackers). This would then allow us to keep using the channel mute feature in S3M like in other formats, but only mute channels in S3M files that are disabled, not muted.

Also,

would it be sacrilegious to have the "Do not process any effects on muted S3M channels" be ticked off by default as it'd make the program a lot more beginner friendly and easier for people to learn trackers

Beginners should not be writing files in S3M format. IT is the default format in OpenMPT for a good reason.

Beyond what I already said in my previous comment, the thing you ask for in the title of this issue is not going to happen. OpenMPT (or more specifically ModPlug Tracker) has been there before (global settings that affect playback but are not saved in files) and it was terrible. When your global settings are different from my global settings, A file you create will sound different on my machine. Absolutely bad idea for playback parameters that have a profound impact on how pattern commands are interpreted.

"Note that there's the "Misc.SaveChannelMuteStatus" hidden setting that you can disable so that the mute status is no longer saved in IT / MPTM / S3M."
Okay so I don't know how to do quotes so I might be doing it wrong, but I don't believe that's what I'm referring to, when I mention the asterisk of shame I meant how in order to get around it you either need to change the starting tempo/speed or add new commands into the channels, which modifies the file and causes it to need saving.

"Beginners should not be writing files in S3M format. IT is the default format in OpenMPT for a good reason."
Well it isn't really a problem when you're writing in S3M at all, it's mainly when listening back to a song. Let's take Big Jim Voyage to Eternity bj-vte.s3m, if on pattern 5 I mute all of the other channels besides 6 and 7 to hear the main lead isolated, then when I play it it's going to be at 6 Ticks per row instead of 3 and will therefore play at half the speed. So what I would normally do is have channel 1 unmuted and then immediately mute it after, which is extremely annoying. Meanwhile, in a-windf.it pattern 12 if I just want to listen to the lead in channels 25-28 then I can just do it and the tempo works fine without having to have channel 30 be unmuted (which I know contains nothing but I mainly listen to S3M files so I couldn't think of any file of .xm or .it format that does things to the tempo).

"As outlined in this forum post, what I would like to have eventually is the possibility to distinguish between muted and disabled channels in OpenMPT; muted channels would still be processed (like in IT), while disabled channels would not be procesessed at all (like in Scream Tracker 3 and a few other trackers). This would then allow us to keep using the channel mute feature in S3M like in other formats, but only mute channels in S3M files that are disabled, not muted."
I mean yeah, that'd 100% fix the issue, how's the progress on that going? :)

Quotes are started by putting a ">" character at the start of the line: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet

Okay so I don't know how to do quotes so I might be doing it wrong, but I don't believe that's what I'm referring to, when I mention the asterisk of shame I meant how in order to get around it you either need to change the starting tempo/speed or add new commands into the channels, which modifies the file and causes it to need saving.

This is purely for creating your own S3M files, not for modifying / listening to other people's files. I was referring to this specifically because of the "accidentally saved muted channels".

I mean yeah, that'd 100% fix the issue, how's the progress on that going? :)

The more often you ask, the longer it will take.