Okay, I'm probably going to come off a bit blunt and killjoy, but...
I don't see how retrofitting Typhons would work out seeing as they don't play nice with beams. A cool explanation would be something along the lines of the Zods developed some new type of (non-beam) ship-to-ship weapon which is only in certain situations and just slapped them onto the old hulls because it was cheaper than building a new hull design for them. I wouldn't call them the primary battleships, though they could be cool artillery or gun-platform pieces which despite being old, outdated hulls (and get mauled in a straight up fight), still find a niche in the navy. That would provide a more believable, and (IMO) more interesting dynamic.
Also, I know your handle is Apollo, but did you
really need to bring back the Apollo? It's probably the least likely of the FS1 craft to be brought back in a derivative form - I don't understand why that would ever be necessary when there is the Perseus, which for all intents and purposes is just better than Apollo: just look at the stat!: Everything is either identical or better. From that entire paragraph you seem to be ignoring pretty much the best all-round GTVA craft of the FS2 era! A more logical step would be to shift the Perseus (or an upgrade of it) into Space Superiority, then introduce a new ship in the true interceptor role.
Between these two I'm getting the feeling that you just really like your FS1 ships, but you're not going to make a
-level story if you're just going to "fanwank" and invoke "magic retrofitting makes previously obsoleted designs suddenly relevant again". That...kind of kills suspension of disbelief really hard. It's also very reminiscent of terribad n00b fanfiction writing (mainly because those things have tons of this). You probably want to steer as clear of that camp as possible.
If you want to do stuff like that without penalty do a TC set in an original universe. Then you can go "i liek this ship design so i maek it op" with (little to) no consequences.