I thought the situation sounded familiar!
As said by others on here, there is no separation between VFR and IFR whether the IFR is flying on a SDR* or not, in class G airspace.
In the situation you describe, I would imagine the ATCO had issued specific traffic information to both parties and quite possibly the ATCO may have slightly delayed the departure until s/he could see the over flight and or was certain that there was no risk of collision, which is what an ATC service is all about after all.
Regarding the not less than 2,300ft part, normally an over flight is asked to overfly not below 2,000ft (providing VMC can still be maintained of course) this is to keep the over flight out of the way of the Tower ATCOs circuit traffic and above the final approach and immediate climb out which is the whole point of having an ATZ however, I suspect one the few trainees may have been on at the time and possibly slipped up and asked for the wrong level, I suspect this was discussed during the trainee's de-brief by his or her OJTI.
I've personally never heard anyone restricting a VFR over flight to not below 2,300ft given the fact that they also can't go above 2,400ft so I suspect a trainee must have been on at the time.
*Standard Departure Route similar to a SID but for us poor people that do not have controlled airspace!