I have turned off the power armor mk3 in the startup settings and was greeted with the following screen when loading my save. I think this is unintended.

It is intended. Because all my tanks technologies are having their corresponding power armour technologies (power armour, PA MK2, PA MK3) as prerequisites. Otherwise, there will be error about tech tree in game start.
One can have PA MK3 but not tanks MK3; but one cannot skip PA MK3 to obtain tanks MK3.

The problem I have right now is that bob also adds a power armor mk3 and they would be duplicated. I only want one in my game and still have tanks mk3.

The simplest way would be just enable it too, as long as they have different internal name. (Should be the case at least for mine, as my PA MK3 is prefixed with "Schall-". So there should not be any game-breaking conflicts. Just use only one of them as your body armour.

There are at least 4 mods (perhaps a ton more that I never have time to check) that claimed to provide PA MK3. It is simply impossible to change my tank tech prerequisite to be based on what mods the users are using.
Also, different armour mods have varying definitions of what MK3 are. Some are easy/cheap to reach; while some are really too much grid space IMO (I consider that to be too OP/cheaty).
Hence it is not feasible to change my tech prerequisites and costs to be based on other mods, without breaking tech tree consistency.

Can you just add some code for bobs? I don't really care about the other mods.

There is no documentation about Bob's mods. It requires exploring and studying his mods to find out his settings. Further balancing may be required if Bob's mods have a different setting of MK3 weaponry. That sounds like a massive time sink, for a mod author who has never touched that.
Time and energy is what I absolutely lacking.

So I would leave it to players who understand and love Bob's mod to add the compatibility code.
If you or anyone have an already working compatibility code, I will be happy to put that into my mod.
(Or if someone decide to rather make his/her own compatibility mod, it is also fine.)

Further balancing may be required if Bob's mods have a different setting of MK3 weaponry.

it costs no space science or low density strcuture. Don't think this is a problem or you just change the MK 3 armor to MK 5 which should be expensive enough.

Yeah, so I probably patch this into a comp mod in the follow days. I let you know when I am done.

Yeah, so I probably patch this into a comp mod in the follow days. I let you know when I am done.

Yes, that would be cool. Please let me know when time comes.

Further balancing may be required if Bob's mods have a different setting of MK3 weaponry.

it costs no space science or low density strcuture. Don't think this is a problem or you just change the MK 3 armor to MK 5 which should be expensive enough.

This is exactly what I meant by leaving it to players who understand and love Bob's mod. I have totally no idea on how the balances can go, but it sounds trivial (or at least relatively much easier) to you.

So the first version is out here https://mods.factorio.com/mod/STbaAB .

It still needs some more tweaking like removing duplicated items and testing if it causes crashes.

So nice!
I have added a link both in mod main page and discussion page. More AngelBobs players should be able to see your work.