One difference between a good handbuilt and a std machine built wheel is the selection of rim.
Rims come with some variance, some are flatter than others. Machine builders just use them all. Handbuilders can reject the more uneven rims and select the best ones.
Starting with a flat rim means that it is much easier to end up with even tension and trueness.
If your Trek wheel just happens to be made with a rim at the wobbly end of the spectrum, it will never be really strong.