Thanks KootK, this is helpful. I don't share the same concern, but only on the basis that the structure will not bear sustained loading. It will be loaded in emergency situations only, so there shouldn't be separation over time. Any separation that occurs from loading can be inspected and injected after the fact.
The problem I'm having is detailing the base plate connection to the slab below. It's fairly close to the edge, and analysis shows breakout in tension induced by the moment (the slab below is by others, and they don't play nice). I've run that analysis under the conservative assumption that the column (HSS) base is not encased, knowing that if the anchorage works for this scenario, the encasement only adds more resistance.
I like your idea of welding deformed anchors, though it still gives me the similar problem of evaluating what the load transfer actually is through the encased section, and what the reactions at the base of the HSS are. That piece is critical to ensure adequate anchorage to the slab without a breakout failure.