But wouldn't that make say a wave of 1000 MK III fleet ships comparably stronger than the compressed variant of Core Guardians?
It depends entirely on the ratio of compression
My understanding from what you said earlier, and what others have said, is that the compression-to-guardians case actually produces a greater threat than the original ships would have been.
And shouldn't a MK IV neighbor be avoided in the early game?
Generally, where possible, but we can't make it an absolute thing or you're up a creek if all the 2-hops-from-your-HW planets are mkIV. So early-game mkIV planets have to be such that you
can take them with an early fleet if you're smart about it. But if the AI has 5-10 units that are 80% the strength of some of its strongest-individual-unit ships... I don't think that's going to go over very well.
For that matter, 5-10 units that are 60% of that, or even 40% of that, sounds remarkably unpleasant