BackupBuddy developer here: It is absolutely INCORRECT to say that migrating sites to new server is uncommon. BackupBuddy helps users move several hundred thousand sites per year to new servers.
We are already seeing a flood of users encountering this problem attempting to move their site to new servers with older MySQL versions. They of course are puzzled why this is a problem since WordPress states it supports this older MySQL version.
Many users these days practice things such as local development, staging, etc which are good modern practices. WordPress has effectively put a huge thorn in the sides of developers and in my opinion has made an extremely big mistake.