Non-separated layers is what causes people to start to pick and choose features. I've been modernizing platforms for about 15 years now, and my first move is always to identify and correct the areas in the app where the layers are intertwined. Even if that is a 2 year effort, it builds up to a day when you can just pick a layer and move it, and it isn't hard anymore.
But those projects are not about MVPs, or features, or product prioritization. It is nothing but pure tech debt - keeping the lights on for the customers while you work hard to change everything under the covers without impacting them.