I agree. I also suspect that the fine details of Drones hadn’t been hammered out at that point either, which is why we will be confounded for the rest of time by the Sky Rider and the Dark Dragon’s rider 
I’ve been trying to make sense of all this myself, so I’ll just run through my reasoning based on the three relevant quotes from PD1:
Unit 01, activated.
Unit 02, activated.
Commence final program sequence.
At the beginning of the game we hear the voice confirming the activation of two “units”. We can more or less rule out the possibility of one of these being the Blue Dragon, as it wouldn’t have been activated by Sestren / the network. It was also around before Sestren activated the Dark Dragon - it was the cause of this activation, as the memory orb from PDS reveals:
Impurity reacquired…
Eliminate it once more…
…Activation of D Type 01…
confirmed…
Note also that these words of Sestren’s are different enough from the above lines for them to realisitically be two different voices talking about similar things.
Instructions from Unit 01 recieved and confirmed.
All ground units mobilized, initiate operations and secure the area.
When the Dark Dragon nears the Tower, the voice confirms that the Tower is receiving and acting on instructions from Unit 01. The voice almost certainly has to be the Tower’s automated voice rather than Sestren’s, because Sestren would presumably not be taking orders (or even instructions) from one of its underlings; it would be instructing them.
Also, Unit 01 cannot simply be the Dark Dragon, as the Tower would logically be taking its orders from the Drone if anything. (So as I pointed out earlier, Unit 01 cannot be synonymous with D Type 01, apparently for two major reasons.)
Unit 01… Confirmed.
After rendezvous, take Unit to full strength.
This is the bit we haven’t looked at recently: when the Tower and the Dark Dragon meet, the Tower takes Unit 01 “to full strength”. This realistically has to refer to the massive enhancement of the Dark Dragon which occurs at this point. Unit 01, then, can’t really be just the Drone either.
My best explanation is that “Unit 01” refers to the Dark Dragon and its rider. A “unit” can of course contain more than one entity, and as the Dark Dragon and its rider are bonded together throughout the game it would make sense for the Tower to consider them a single unit.
With that in mind, I’d suggest that Unit 02 is the Tower itself; after all, it was activated more or less simultaneously with the Dark Dragon. The fact that the last lines of text refer to the meeting as a “rendezvous” could vaguely suggest that it was a rendezvous between these two vital units, as well.