[quote]The Age of Gods is directly tied to an abundance of 'Mystery'[/quote]

Nope, relative power balance between gods and mortals. This is pretty firmly established by CCC and Extella, amongst others. The gods lost a lot to [hider]Sephyr/Sefar[/hider] including the heavy Ether presence that allowed materialisation and needed a way to address the balance, they made Gil so that people would remain appropriately reverential towards the Gods and reverse this, he decided that humanity's future was better.

Everything else just follows on from that continuing decline of incredible power concentrated in a few entities. It still resurfaces, though; things like the Dead Apostle Ancestors and magical beasts wield all the same power they always have.

[quote]The greatest example of mystery against science is reinforcement being unable to work on a firearm. It is simply impossible to reinforce a firearm with magic due to the fact that the firearm rejects mystery due to being a complex mechanism of science[/quote]

I think that's more because Magi are incompetent and don't understand guns well enough to work out how to enhance them in such a manner.

But if you really want to bring up magic guns: Lancelot says hi with Knight of Honour, Edison literally makes magitech robots with guns in America, there's every Servant WITH a gun... they're eminently capable of being reinforced, magi just don't know [i]how[/i]--seriously, they probably could with something simple enough of a lot of work at it; but why bother? More direct magic works just as well. Kiritsugu is the only magus to heavily use guns and his magical knowledge is mostly time-related due to his magic crest.

Babbage literally runs on science and a Reality Marble that says "screw the second law of thermodynamics".

And again: [i]the translation used is not Mystery.[/i] It is not the concept of being [i]unknown.[/i] Things that work by reducing mystery work by making the supernatural seem mundane (not actually "oh this is unknown") or in Edison's case [i]taking this thing and mass replicating it.[/i] Which is actually a different reason why mystery can be lost--an ancient item, broken and repaired, starts from scratch. Edison's NP is his mass replication philosophy, which replaces one original with lots of built up power with imitations.