I know that, but layer (to me) make harder to do stuff, specially if need to do some key bindings that require more than 1 key (like ALTS, TAB, etc).

This push to do heavy customizations but that create the issue of work only for X machine and X OS. In my case, a do work inside VMs and customers machines by remote software and also need to work in other laptop, so I prefer to not do keymaps customizations at all...

Most of these custom keyboards run the QMK software. All the customization is within the keyboard's software, so the OS never knows. The keyboard is just a plain USB keyboard, as far as it can see.

That said, I think it's a good idea to keep function keys if you use them. There are some keyboards with them, but it's surprising uncommon.