I've not been able to reproduce the Czar issue you mention (even if I activate the total mayhem mod since you mentioned that in your reply), but from the description it sounds like it's broadly working as intended since it's meant to be used to attack ground units rather than air units. So while it might not be optimal (re there being some scenarios where its AA abilities would be good), the difficulty with reproducing it coupled with then the difficulty in having logic that figures out if it wants to have its air to ground attack active vs its AA attack active means it's unlikely to change.
I've fixed the bug with the kennel not upgrading though (will be in the next release).
M28 should build T1 experimental base defences, but I've no plans to have it build other T1 experimental units (e.g. tanks etc.) as M28 is setup on the assumption that engineers can only access experimentals at the T3/experimental stage (not T1-T2) so it'd be non-trivialto add and I'm not clear that it'd have a significant competitive benefit that would justify the extensive recoding required (compared with just getting T2 land or more T1 non-experimental units).