Yes, it's cheating. You are stacking the deck for your home system.
You could start with out with a PQ85 home planet and a PQ78 secondary (or, whatever).
Just with that, since virtually all tiles would be available on both planets, you would be able to build all the construction and econ buildings needed to complete 2 ships per turn. You would also be able to build research buildings that would let you jump far ahead of any competition (two techs per turn - assuming only two home planets), so you would have better weapons and defenses - and everything else - in short order. You also have room for farms and morale buildings, so you can quickly build up the population while keeping them happy. That also helps if an enemy invades, since your population is too high to overcome without many troop ships - and too happy to defect.
But you could not stop there if you wanted to win a game. In order to win a game you have to take other planets (unless you simply go for a tech victory). And every planet taken means another tech produced per turn (up to a certain point), so a tech victory is all too easy. (I always turn that option off)
If you're smart, you'll research the research techs first - because they allow you to build the research buildings that produce the most. Once you can produce enough research to gain the advantage in weapons and defenses (no matter the odds), you have won the game.
You say... 'mod the game in certain ways' to give you higher PQ home planets. How, exactly, are you doing it? Is it a custom map (a real pain in the butt), or another way?
I don't mess with custom maps, because they are such a pain to create. But, I do mess with it the only other way (that I know of).