The answer to this depends largely on how you define "engine" but the basic answer is "kinda".
To me, an 'Engine' is a collective of systems that intentionally rely on, or compliment one another. Its normal that plugin developers would ensure compatibility at least with their own systems, some of them would likely fully replace existing features, where other plugins might only further enhance the default engines behaviour.
IMO, an 'Engine' has to contain a significant number of systems. Like, having a 'battle engine' or something with only small changes to the battle system is silly; however, having a collection of large systems that fully overwrite every possible aspect of battles, and give you more control over how they function and flow ~ thats a different story..
The coders who said the engine mean they put a lot of work like Yanfly Core Engine (YEP). Therefore, the plugin modified or extended many functions in the main code itself. "Engine is made for RPG Maker MV. This plugin functions primarily to fix bugs and to allow the user more control over RPG Maker MV's various features, such as the screen resolution, font, window colors, and more."
I say depends as you are aware some plugins do not get a long because it might not recognize each others, working different methods, or other headaches that the programmers will find when they are coding in general lol.
I've been trying out Fell Seal: Arbiter's Mark, and it has an interesting approach to consumable items - you get a limited inventory that is automatically refreshed to max limits (1 or 2 each, craft to expand + improve effect) at the start of each combat. It's a mechanic that goes against the common urge to hoard consumables.