It is like saying return all functions in one place, or other habits. There is one type of design where you might want to do this, one that is purely interrupt/event based. There are products, that go completely the other way, polled and not even driven. And anything in between.
What matters is doing your system engineering, thats it, end of story. Interrupts add complication and risk, they have a higher price than not using them. Automatically making any design interrupt driven is automatically a bad decision, simply means there was no effort put into the design, the requirements the risks, etc.
Ideally you want most of your code in the main loop, you want your interrupts lean and mean in order to keep the latency down for other time critical tasks. Not all MCUs have a complicated interrupt priority system that would allow you to burn a lot of time or have all of your application in handlers. Inputs into your system engineering, may help choose the mcu, but here again you are adding risk.
You have to ask yourself what are the tasks your mcu has to do, what if any latency is there for each task from when an event happens until they have to start responding and until they have to finish, per event/task what if any portion of it can be deferred. Can any be interrupted while doing the task, can there be a gap in time. All the questions you would do for a hardware design, or cpld or fpga design. except you have real parallelism there.
What you are likely to end up with in real world solutions are some portion in interrupt handlers and some portion in the main (infinite) loop. The main loop polling breadcrumbs left by the interrupts and/or directly polling status registers to know what to do during the loop. If/when you get to where you need to be real time you can still use the main super loop, your real time response comes from the possible paths through the loop and the worst case time for any of those paths.
Most of the time you are not going to need to do this much work. Maybe some interrupts, maybe some polling, and a main loop doing some percentage of the work.
As you should know from the EE world if a teacher/other says there is one and only one way to do something and everything else is by definition wrong...Time to find a new teacher and or pretend to drink the kool-aid, pass the class and move on with your life. Also note that the classroom experience is not real world. There are so many things that can go wrong with MCU development, that you are really in a controlled sandbox with ideally only a few variables you can play with so that you dont have spend years to try to get through a few month class. Some percentage of the rules they state in class are to get you through the class and/or to get the teacher through the class, easier to grade papers if you tell folks a function cant be bigger than X or no gotos or whatever. First thing you should do when the class is over or add to your lifetime bucket list, is to question all of these rules. Research and try on your own, fall into the traps and dig out.