In AoW3 there was next to 0 difference between picking, for example, human dreadnought or elf dreadnought or goblin dreadnought
Well, no, because AoW3 actually has multiple mechanics and systems that go beyond race and class choice whereas in PF that's all there is, because all the AoW3 incline is either completely gutted or just plain gone. Both games have exactly the same approach of certain class units being different depending on the race (which is cool). Like I said, the main difference is that AoW3 puts a very strong focus on the class, while in PF it's the race.
I have voiced my opinion on the mod system a lot of times (tldr: nice idea, mediocre execution, the reality of how the game plays turns it into largely meaningless theorycrafting), but the main issue I have is that despite there just being choice of race and class, there's very little interesting combos in PF. The class is often literally obsolete and something like hereditor, for example, was just "spam only hereditor units... or don't", cause it synced with literally nothing before the final dlc race arrived. There are multiples examples of classes giving almost fuck all to certain races and for the rest it's usually just "yeah, having some units/mods that share dmg channel might be good". Mindblowing. I know there are some exceptions to this, like my favorite syndicate+promethean, but they're far and few between.
AoW3 has race + class + magic school (unless I'm forgetting something), while PF has race + tech + neutral faction alliance. The choices you make in PF make a bigger impact on how your unit roster looks like and behaves than AoW3.
In AoW3:
-The only way race choice impacts class choice is racial modifiers of units (orcs deal slightly more melee damage, goblins have slightly less HP but are slightly cheaper) and racial governance bonuses, which are not that interesting (I looked it up - most bonuses up to tier 3 usually amount to something like your specific tier 1 or 2 units gaining an extra point of damage or some bonus HP. The only ones that can truly synergize with your class units appear late in the game and affect all units of X type)
-The only way class choice impacts race choice is through global upgrades, like dreadnought giving all cavalry pistols or priest giving healing to all caster units, of which there are very few. Necromancer is an exception to this, but necromancer kinda just plays its own game. It affects the chosen race significantly, but it affects all races in pretty much the same way.
-Magic school choice doesn't really affect your race/class units, but can give you a few new units in the form of summons. Some schools have upgrades that can give some permanent bonuses, but mostly it's just spells that can give you an advantage in combat.
In PF:
-Race choice can affect your secret tech units by allowing you to put your race specific upgrades on those units
-Reverse also applies
-Upgrades can change how the units work in significant ways. For example, voidtech has a flying support unit that can heal and reposition units. It has an energy weapon attack. I remember playing 1 game as energy weapon-focused assembly and I gave this thing an upgrade that energy weapon attacks chain to additional targets and another upgrade that made them also stun enemies. I also allied with the imperials neutral faction, which gives that shield upgrade, which gives a unit more armor the more it's attacked during a turn, so I also put it on that thing. This turned a primarily support unit into a strong damage dealer that was also pretty annoying to kill. I also gave the same upgrades to the energy weapon units assembly has by default, so my army consisted mostly of those + flying voidtech supports. Another example: you mentioned how hereditor (or whatever the fuck those things were called, let's just call them space necromancers) tech doesn't really work with any of the factions, but I remember playing a game with my friend where I went lizardman necro and gave my units a bunch of necro defensive upgrades that charged when the units were attacked and then I could use charges to buff their defensive stats, which made my army very hard to kill and it worked well with the lizardmen because a lot of their units are low range.
Note that neither AoW3 nor PF has something like unique race+class/tech buildings, units or upgrades which is something I truly want.
Now don't get me wrong, I still think AoW3 is overall a better game than PF, but I found it more fun to fuck around with the factions' unit rosters in PF due to stuff like the examples I described.