Problem joining log-shipped secondaries in STANDBY to AlwaysOn group
When restoring WITH STANDBY SQL Server has to undo uncommitted transactions (the relevant data pages get written to the undo file that you specify). The NORECOVERY option does not care about the state of the log, or performing any potential rollbacks, that would happen if the database were recovered. Because the two leave the DB in different states you would have to reapply the final transaction log WITH NORECOVERY in order to be in a good state. There's an excellent write-up on this at https://askmesql.blogspot.com/2011/01/log-shipping-norecovery-vs-standby-mode.html 

As for your monitoring software, I would recommend putting in a temporary exclusion for certain databases, or even instances while getting the AG setup so that you do not get those spurious alerts.