While unit itself is amazing to play with (in RA3) i'm afraid that the main reason of its awesomeness (namely Black Hole generator) would be impossible to reproduce even with the power of Ares. So i highly doubt it would be implemented into MO.
On the Boidmachine topic, IMHO it having practically infinite range is cheesy AF. Point, click, delete units with 0 risk. Give the damn thing actual range. Make it very long, but still short enough so that it can't stay in the base and reach everywhere on most maps.
The activation sound is loud enough to be heard and there is indicator for where it's being fired. Most of time in your forces, so just move them away. There is also one more thing - being even 1/4 heigh above boidmachine completely screws up[ its targetting. High ground for the win!
Here is an example of how badly Boid can miss in mentioned before scenario:https://youtu.be/QZJgK6LnvBQ?t=1521
However it needs a significant damage buff, say 165/300 => 265/300.
There is no way this is happening. Athena's have huge impact damage to point, where couple of them can decimate buildings with ease. While in 1 on 1 tests Athena seems to be weaker than Prism, it gets better with numbers. 2 Athena/2 Prism are on par, while in 3 Athena/3 Prism it's the athenas who are on top.
If i had to make a change, it would be on Mercury - replace damage buff with RoF buff. That's all.