If I retreat an enemy unit I control using Hostile Takeover, does the unit still get recalled to their base?

To answer your question: No, the unit will not be recalled to its base.

When you use Retreat on a unit you control (even if you only control it temporarily via Hostile Takeover), the unit is returned to its owner's hand. Because the unit has left the battlefield and moved to a non-board zone (the owner's hand), it is no longer present on the battlefield to be recalled.

Here is the breakdown of the interaction:

1. Control vs. Ownership: As established in RiftJudge FAQ #7666 and #3919, when a possessed unit is returned to hand (by Retreat), it returns to the owner's hand, not the controller's hand.
2. Recall vs. Return to Hand: A "Recall" (as specified in the text of Hostile Takeover) is a specific game action that moves a permanent to its base (Rule 450). Retreat is a separate effect that moves a unit to its owner's hand.
3. Effect Resolution: Once the unit is in the owner's hand, the "recall it at end of turn" instruction from Hostile Takeover no longer has a valid target on the board to act upon.

Summary of the result:

• The unit returns to its owner's hand.
• The owner of the unit receives the benefit of the Retreat (they channel 1 rune exhausted, per FAQ #3919).
• The unit is not recalled to its base, as it is no longer on the battlefield.