Yes the bulky seams do cause a problem in making the blocks fit. I believe you have to press in such a way and join to give the least bulk at these junctions. Also, fabric weight and thread weight can make a difference. This is why it is always a good idea to make a small practice sample and then adjust according to the nature of the fabric and thread. I find that heavier weight - even #50 can cause more space to be taken up. Even one eight in bobbin and the other in top can give problems. One has to experiment.
I tend to grab any thread handy when thread runs out and if it takes up more space then switch back etc etc etc.
There is no sure way - need to experiement. Then, if I do have a bulk problem, I may shave a bit of one seam allowance to reduce the bulk.