Have you played
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? It's been around for a over a decade with a very consistent update schedule, and transformation is a core feature.
Two things to keep in mind are that it's currently written in Inform (a Godot port is currently in the works) so it generally uses a very Infocom-esque control scheme, and it's
very furry.
I suspect that RPG Maker itself might be largely to blame for the difficulties in implementing the sex system in your game, to be honest. I haven't messed with it in detail for a while, but last time I worked with it it didn't seem very well suited for anything outside of the general JRPG formula. Granted, anything is possible with plugins (it sounds like you were able to get it to work with considerable effort), but it's largely going against the grain.
A transformation system is conceptually pretty easy to implement if you have complete control of the engine. At its simplest, it's essentially a matter of making body part objects for X species and attaching them to Y character instance in some way or another. It's a lot more tricky to design handwritten sex scenes around that, as the writer has to take note of how large the player is, how many dicks/pussies they have, the length of their hair, whether or not they have a tail, and a myriad of other things depending on the exact content. I've written some practice scenes in the past year or so using Twine, and constantly having to keep in mind things like the position of the player's head relative to another character's body during, say, an embrace can be pretty draining.
I'd argue that LT's dynamic sex system is kinda cheating, but it's very pragmatic given Inno's general approach to the game's flow. Rather than having richly written interactions designed around whole characters, the interactions in LT are based around interactions between body parts at a given pace (rough, normal, and gentle) and against a set of fetishes (though it largely boils down to hate/tolerate, as everything outside of that is purely mathematical). It's good in that interactions generally make some degree of sense without requiring too much development time or restricting player freedoms, but IMO it tends to lead to interactions that are largely forgettable. It's good for a quick fap in the moment, I suppose, but it results in a distinct lack of personality. Everyone with vaguely similar parts behaves identically at a given pace.
The only really unique scenes are stuff like the absolutely obscene hand-holding scene with Rose. There's a handful of them in the game, and it shows that the dynamic sex scene can really pop when it's fed the right stuff. The problem is that those scenes are few and far between.
I think a lot of that would be mitigated if more care was taken with regards to named NPCs. There was a lot of potential for character and world-building with the now-scrapped companion system (assuming sane limits were put in place to keep it from becoming overwhelming), but I think it's safe to say that ship has sailed.