
Was the antimatter merely the primary of a larger yield device?
I don't think so. If it primed a non-antimatter explosive, Spock wouldn't have specified a "matter-antimatter blast" as the exact mechanism that rips away the atmosphere... And if it merely primed a greater amount of antimatter, then Kirk's one-ounce order would make no sense.
Personally, I think that once the whole Federation went metric, the definitions of things like "mile" and "ounce" were reworked a bit. Or then simply forgotten, so that "an ounce" would become the accepted expression for "as much as you can hold in your hand" or something like that.

Why not just beam down the blood and use photon torpedoes when the bait is taken?
The thing was known to be good at evasion, and to have experience in evading photon torpedoes. Better not give it the luxury of advance warning with already familiar torps approaching from a distance - or risk things like missing-by-ten-feet(meaning the creature might have time to become transparent to the incoming antimatter blast), or torpedo failure, or whatnot. A simple demolition device was the easiest way to go.
What was less clear was why two people had to go down to the surface with the bait and the bomb. But perhaps both Kirk and Garrovick had figured out that the blood would not be enough of a bait, and had firm plans of using themselves as the luring agent, yet couldn't say this out aloud.

How did the creature extract the blood from the sealed container?
Would it be sealed? I mean, our heroes may have figured out how the creature got into the starship - apparently not simply by becoming transparent to matter, but by exploiting a weak point in the ship's outer shell. Starships are likely to have those, since they only have to resist one atmosphere of internal pressure; the critter could have pushed through a membrane in the ventilation system that resists five atmospheres but allows the sixth through. Similar casing could then surround the bait.
But that's probably too much finesse. We already know the critter has the ability to alter its physical nature a lot, becoming invisible to sensors, at least seemingly turning into other substances altogether - and probably using these qualities to become immune to phasers and antimatter blasts as well. It would only stand to reason that it could become transparent to things like starship shells or blood containers. Perhaps just part of it flowed into the container, then reverted back into something that could interact with (eat) blood, then went transparent again and joined the rest of the beast, delivering a load of satisfaction.
Whichever approach it took, this would be in line with the rest of the drama in the episode. The audience should expect vampire-like ability to go through walls from this space vampire cloud!
Timo Saloniemi