"I can advised [sic] you that the work needed to put the favicon live was complicated by an old environment (which has since been updated) that caused issues and extended the time taken to carry out the work."
Maybe this is a euphemism for "bunch of old people who don't know how the internet works but were put on the web site steering committee anyway and made a bunch of of absurd requests that had to be fulfilled in order to get approval".
Quick and dirty solution, for each favicon you'll have a different virtual host inside Apache.
And I fail to grasp the situation where you've got multiple subdomains setup inside the same virtual host config (through ServerAlias), but still having different favicons. But even for this case you can probably come up with something based on mod_rewrite.
What?