The patch in question doesn't change content at all beyond fixing two way teleports: no further change was made, nor any change that heavily or passively compromised the original integrity of the map pack. The modification of CSCM for Mapchella that removed MM5CHAX and renamed the pk3 file did in fact also remove the script that kicked people who used SR50, as mentioned
here.
When I asked (I didn't make this by the way, I requested it to Jax and discussed about it with Celebi if you wanted to know) why MM5CHAX was removed, I was explained that MM5CHAX
might have possibly been blacklisted because of an unexplainable(?) crash that involved bots, which is or was an issue shared with the core version of the map, which in turn prevents or used to prevent bots from entering specific areas of the map: perhaps BE reacts to this automatically by blacklisting servers that crash in such fashion. This
and the anti-SR50 script were the suspected reasons for the blacklist back in 2014 for Mapchella, and as such both were removed from the original v5b pk3 for safety reasons. The patch takes that modified pk3 into account.
Nothing was radically changed with this patch, it only fixes compatibility issues with two way teleports so the maps are playable for current versions of Zandronum: it's the alternate version of the pk3 that has the actual changes, and so to be as safe as possible for BE hosting, Jax took that pk3 into account. If MM5CHAX has no merits to be removed, it could be as simple as updating the patch to take MM5CHAX teleports into account, if there were any in the first place.
EDIT: IIRC, you can't host on BE with the original blacklisted pk3, so there's also that: the patch is for the secret alt pk3 that CAN be hosted on BE, which also coincidentially removed one of the maps. If we wanted to make hosting possible while also keeping MM5CHAX, then we would've just released an update...which really isn't something any of us should do except those who originally managed this map pack. Just a humble patch that works with what we've got.