I know the way I am fully constraining it right now is not the best way, but I was not sure how else to simulate threads holding the part in place on both ends.
The best way to tackle this problem is to think of the idealized kinematics of the design assuming there is no friction. A threaded mechanical joint prevents on-axis translation, while everything else is technically free to move.The problem is that, for a finite element model, you need to constrain the system to prevent rigid body motion. This is where using springs and links or symmetry comes into place.
When I say that I'm ignoring the high stress areas, I mean that if I get a high stress concentration, I will ignore those results. They still happen, but when I present my results I classify them as outliers.
That's OK, just be sure that the stress concentration is due to modeling conditions and that you use an Isolate for Exclusion mesh control with some insulating elements. Singular elements can pollute the stress results you want to simulate if they're not handled properly.
I am performing the FEA to prove hand (and by hand I mean excel) burst/collapse formulas. The hand calculations are not able to account for cutouts, and this is where the FEA can provide more accurate information about whether a part can withstand a pressure or not.
Collapse or burst? Are we talking about a mechanical instability here (like buckling)?
Also keep in mind how load transmission can effect the results near the threads. Again, whether or not this is a problem depends on the design and where you want results. The image below shows two 3D models with and without threads and using a weighted-link with a zero-length spring, and a 2D axisymmetric model with contact.
