I don't think there has been huge issues with incompatible ISAs on ARM. If you'd use NEON extensions, for example, you might have a C-implementation that does the same if the extensions are not available. Most people don't handwrite such code, but those that do usually go the extra mile. ARM SoCs usually have closed source drivers that cause headaches. As well as no standardized way of booting.

I haven't delved super-deep into RISC-V just yet, but as I understand these systems will do UEFI, solving the bootloader headache. And yes, there are optional extensions and you can even make your own. But the architecture takes height for implementing an those extensions in software. If you don't have the gates for your fancy vector instruction, you can provide instructions to replicate the same. It'll be slower on your hardware, but it'll be compatible if done right.