If I choose to take Killbane’s mask, am I completely locked out of the Apoca-fists

Choosing to give Josh over to Cyrus results in you receiving a "City Takeover" bonus, separate from the City Takeover upgrade. Choosing this bonus will not lock out the regular City Takeover upgrade.

Using this bonus allows you to take control of one large area of the city of your choice. This area is outlined by a bold purple line, includes more than just a single Diversion/Property, and is named, like Loren Square or Sunset Park (basically, the neighborhood division lines).

It does not have to be within Morningstar territory. Taking control of the area will automatically complete all Diversions in the area, as well as automatically give you all properties in the area.

When you buy and apply the Unlockable Pack DLC, you will get all of the rewards of all of the possible mission choice rewards. So, for example, you will get the lump sum cash bonus AND the percentage cash bonus from the The Ho Boat mission. Missions usually have a static reward with no choice involved. Such missions without optional rewards will not be unlocked automatically via the Unlockables Pack DLC.

The optional bonuses are all unlocked and applied once you are past the third mission of the game which involves assaulting the Steelport guard armory for munitions ("We're going to need guns"). This is also when you first exist in Steelport while not bound to a mission, and when you spawn in Shaundi's ex's crib. The unlocks will appear as rewards screens, like upgrades or (post-)mission (completion) rewards, a few seconds after you've spawned.

There is no choice; they are involuntarily applied at that point. The biggest downside to this is being forced to use a City Takeover. If you want it to have the least impact, I recommend choosing Arapice Island (in the mid-west).

Update: Well, I finally got around to recording the footage.

This is me unlocking every SR3 DLC. The unlockables pack should be the rewards regarding the gangs. It is also responsible for me having to use a City Takeover. Note that this occurs (at any point) after the third mission.