Well, first of all, the universal form is not how Krsna "really looks". That is a common misconception. Krsna's form as cowherd by with blue color, two arms, flute - that is the Supreme Personality of Godhead and it is His eternal form of bliss and knowledge. Isvarah Paramah Krsnah Sat-Cit-Ananda Vigraha. Isvara and Parama refer to the Lord as Supreme Controller. Sat means eternal existence. Cit means knowledge. Ananda means bliss. And vigraha means form.
All forms of the Supreme Lord are one and the same Supreme Lord. Therefore there is no question, "Did the universal form have knowledge that the 2 armed version was showing the universal form to a devotee?"
The universal form is doing something different from Krsna's Personal form. That should be obvious. But that doesn't constitute an independence or a separation. Discernment is there. That's all.
Krsna showed Arjuna His universal form. Plain and simple. It wasn't some replicated vision, but it was certainly presented for the "vision" of Arjuna.