Both the accelerated healing and spontaneous mutation would count as uses of his powers — the passive biological changes will be fine, but anything where there is a clearly "active" use of powers will count towards the maximum of two uses. In Ade's case, it doesn't matter if he uses them on purpose or if it is automatic: it is an active alteration of the state he has been, through the use of powers, which then counts.

We hope this helps clarify it!