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That's a really good question... I'm still using RPG Maker to define the weapon and monster stats via it's database and also visually creating some events that I'm using as "prefabs" that can then be dynamically cloned to populate the levels.  It allows me to create a static level that I can populate and test out the interactions before turning on the procedural generation.  Also, even though the built-in battle system is not being used, that logic is still all present and the damage routines can be called individually which is what I'm using to resolve combat and potion effects.  I think if I continue down this path, I'll mainly be using RPG Maker more and more as just a library of routines instead of how it's normally used. 

Also, even though RPG Maker has it's own built-in level designer, I've switched over to using TileD for designing levels in some of my other experiments since it has more versatility.  In fact, the procedural generation in this roguelike are actually populating TileD level maps that are being rendered with the RPG Maker engine via a third party plugin.

Regardless, I think RPG Maker provides a real nice jumping off point to get something going quickly, but it also exposes all of the code so you are able to really customize it way beyond how it was originally intended to be used.  Also, with this last version (MV), it's finally cross platform and web-enabled.  It was pretty much a non-starter for me before that point.