Let me see if I can help out a bit more on B and C
Alien ranks, unlike normal levels, do not give you any IPs to spend. Instead you will receive Alien Perks (similar to the Shadowlands perks which you gain every 10th level (10, 20, 30, etc) and at each shadowlevel (201, 202, 203, etc)
If you press CTRL+P you will get an overview of the perks available to you, the ones marked in Green
are Alien perks. Most profession will have: Atleast one in their Profession Perks, atleast one in their Group Perks and all professions have the same in the General Perks.
For instance as an adventurer I have access to:
- The Profession specific Alien Perk which adds a bit of nano, a bit of evades, some HP and a few other neat things in addition to two perk actions
- The Group specific Alien Perk Line which gives me more Multi Melee and Multi Ranged skills in addition to a few nifty perk actions.
What Perks you get depends on your profession, but many of them are very handy, and also the Champion lines are nice for just about any class (adds to specific weapon lines or to nano skills)
The example you provide with Stamina is correct to some degree. Let me try to explain.
The natural breed cap is hardcapped at X stamina (in the case of an opifex it is 480 (until you hit the Shadowlevels, where you can again spend IPs in attributes <3 ) ) This basically means that you can not get any more stamina than 480 from purely sinking IP into it. On top of that comes your equipment, perks, research, etc.
In the case where you had 480 stamina already IPed and finished the research for +5 stamina, you would then gain automatically 5 stamina.
In the case where you had 300 stamina and then research the +5 stamina line, you would automatically gain 5, adding up to a total of 305.
So to put it bluntly, the breedcaps simply limit the amount of IP you can spend on a skill/attribute, ontop of that comes everything you have equipped/perked/researched
For instance my adventurer has 997 strength in his current equipment at 220 even though the breedcap at 220 is 772 strength, the additional 225 strength comes from what I mentioned, perks/equipment/research and when I had equipped/researched/perked this would not matter because the math for that is applied after the IPed skill/attribute
When you research the skill increases does not matter, as it will not affect the caps in the way you describe, but simply add to the current attribute level total.
You'll have to excuse me if I might be slightly confusing, but I am not the best person at explaining game mechanics
I hope I was atleat clear enough that you understood the basic idea, if not please ask again for anything that I might need to clarify further