Is there some other fundamental underlying non-compatibility with the light from the Fibre strands and the electonics in an alarm system that I am missing here?
Nothing to do with light and fibre, unless you’re in need of some gut health and digestion improvements.
Note that VoIP will run over the top of any IP based connection - be it ADSL or 4/5G cellular. We will all be running some form of VoIP after PSTN gets withdrawn in a few years. That could indeed still be served on a copper pair, where there’s no FTTP.
You’re relying on the ATA to provide a fully 100% compatible signaling interface to/from the alarm dialer. Some folks will know how finicky ATAs can be at these tasks (try getting a fax machine reliably working) - even if the ATA theoretically supports the numerous ways in which DTMF signalling can be sent/received over a VoIP service.
The recommendation with VoIP based circuits is to upgrade to an IP or combo IP/Cellular communicator card rather than chancing it with the original analogue communicators.