Yes this happens in every framework I've ever used. My approach used to be to try to work around it, but now I've got these local exceptions to what the framework does and that is inevitably where problems/bugs pop up. Now I simply say "we can't implement the feature that way in this framework, we need to rework the specification." I no longer try to work against the framework, it's just a massive time sink and creates problems down the road.
It's like designing a kitchen and you don't make all the spaces some multiple of three inches. Now, standard cabinets and appliances will not fit. You will be using filler panels or need custom cabinetry. And anyone who later wants countertops or different cabinets will be working around this design too. Just follow the established standard practices.
I'm so glad software engineering isn't my job. I love solving problems, and I'm somewhat better at using code to do it than my peers (fellow scientists), but I would hate to have a boss/client that says "it needs to do X" and the framework writer (or SDK, ala Android/Xcode) say "no, that hurts my profits/privacy busting".