Considering the gains from even "empty" (no moneymaking industries) colonies, the cost of spamming patrol HQ everywhere is all but insignificant.
Same goes for HCs, until the game is able to punish you in some way for flooding the market with demand (aka when there's 20 units of fuel and 30 hulls available in the whole sector but you alone need 100 and 80) it's a more than worth-it industry slot.
As for the Heavy industry question, it does not matter where it is as long as it's there, the effect of it is faction-wide (even your crappy outpost on the fringe of the map would benefit from upgraded ship quality), do not remember if commerce spawns a military market if there's a military/HC along it, as i'm never using it (i mean it's only here so you can sell things, i'd rather dump my excess ressources at the corresponding industries needing it and the redundant blueprints/survey data at the closest npc market), the industry slot here is not exactly fantastic/
BUT the presence of a bonus market or not is irrelevant, as custom production allows you to command specific ships without any D-mods for extremely cheap (and even some weapons, supplies/fuel/crew to go with it are offered)
Also the pather cells do not matter, they literally don't, consider them a mandatory pitiful -1 stability.
Conclusion: Nothing beat having an impenetrable system full of your own fleets, they're the ones babysitting me now!