Threads created with the thread/hole tools in Inventor are just cosmetic images applied to that face and are not true modeled surfaces as you have found out..
In general a 3d printed thread isn't going to work with typical thread geometry either so many times you need to physically model a thread profile (by sweeping a profile along a coil)..Thats also what the cool orange tool does and last I remembered it was really darn easy to use but didn't really produce a thread form that could be 3d printed reliably..
I personally would recommend modeling the threads yourself as stated above (sweep profile along a coil)..
I'll see if I can find a video/tutorial of that..
But you will need to modify this thread profile on both parts to adapt for accuracy/precision issues/material sag/flow associated with 3d printing..
In the past I've either use a tap or a thread forming screw when I needed threads in a 3d printed part or use a design that negates the need for such..
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Inventor 2023 - Dell Precision 5570
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