There is no danger in this, and yes, notes are per-request. This is a pretty common method of passing data between Apache extensions. The performance hit should indeed be negligible.

I'm not sure what other advice to give you; this is a good way to use notes, and a good way to pass data between sub-requests and phases of a request. I can't say I particularly like the concept of running a PHP program as an API to a lot of business logic, but given your description it doesn't look like you can get around that easily.