If you can't guarantee that every layer below you is absolutely reliable, then you need to assume that everything below you might be broken, and that you need to handle it. You can't start with the mindset that everything works below you, and have everything above you also work fine.
The fact that we have people with the mindset that everything below them is broken is the entire reason that these kinds of issues get detected and fixed.
Yeah if you try and work around broken PMTUD though you're going to mess up your application layer protocol SO bad...
EDIT: I suppose you could rewrite TCP MSS on your own firewall or drop MTU on all web servers.... but of course if you're going to reconfigure your firewall / intefaces, you may as well just fix the problem - which was caused by poor device configuration in the first place.
If you can't guarantee that every layer below you is absolutely reliable, then you need to assume that everything below you might be broken, and that you need to handle it. You can't start with the mindset that everything works below you, and have everything above you also work fine.
The fact that we have people with the mindset that everything below them is broken is the entire reason that these kinds of issues get detected and fixed.