+1 Million. Not to mention is just promotes Truck City cancer in team games. Let's require Howies be built outside base so they are vulnerable. Great, now let's cover it with a Flak gun and healing+reinforcement point so that unless you nuke it with an offmap it's impossible to counter conventionally. Much fun will be had by all.
It being a tier structure makes it a bit of a double edged sword. It's "free" in that it doesn't cost population, and that it will exist in 90% of OKW games. The fact, then, that OKW get a "free" defensive structure they can use to help lock down a point is very strong.
On the other hand, it being a tech structure makes its loss absolutely devastating to OKW, same with any of their other buildings... which is why you don't really see them far forward all that often (Despite them nominally taking the place of structures and units other factions have access to, that DON'T affect tech levels when destroyed). It has almost twice the HP of the allied equivalent (Bofors, 28% more when the Bofors hits Vet 3) and more armour, though does lack brace.
I think it's almost a similar story to Howitzers, its rather binary. If you get the opportunity, it doesnt stand up to a huge amount of abuse from AT guns or similar units, and it can be obliterated with no counterplay with some offmap solutions... but it can be pretty oppressive if, like you say, OKW manage to get a little city/defensive position set up, and you don't have adequate offmaps.
Arguably the Bofors is similarly annoying, but does cost Popcap, and doesn't come during normal teching... though the loss of a Bofors doesnt hurt the Brit anywhere near as badly as the loss of the Flak does an OKW player.
I think if the flak were to be made weaker, then either replacing the Flak HQ might not want to be so costly (For tech purposes, the gun itself could be rebought for a premium, but the truck itself would re-unlock tech), or if it remains the same price, don't require it to be rebuilt for OKW to make at least some of their armoured units. The latter option obviously makes the FlakHQ an almost throwaway unit though, with next to no penalty for its loss, so isnt really viable.
Alternatively, make the Flak Base a Bofors-like "unit" that can be built, and has an associated population cost, and make the Schwerer Panzer HQ a non-combat structure. A tech structure being a combat unit is a cute idea, but I think it has a few too many problems in practice.