TQ secondary not opening up all the way

Correct, vacuum drops as throttle opens.
The air door on the secondary doesn't open all the way because the flap serves to create enough vacuum (not technically, but....) to draw fuel into the carb.

I don't think it's correct for it to stop against that shaft spring though.
You said it right. The air door does create vacuum....or I guess more "technically" a low pressure area that allows atmospheric pressure to "push" fuel into the secondary venturis. That's close enough to dang vacuum for me. lol You're also correct in that the linkage does not limit the vacuum door opening. That is handled by a bendable tang on the driver's side of the secondary opening. The tang is bent to limit how far the door opens.