USB devices not working if I solder them through wires
Probably extra capacitance and inductance from the DIY breakout is violating high-speed USB specification


Nope. The problem is impedance. USB 2.0 is high frequency enough to have signal refections at any point with significant impedance mismatch - and your breakout will have a rather large impedance mismatch. 

Remember that impedance largely depends on physical properties like size and distance (to each other and ground), so a "breakout" is never a good idea for any HF transmission lines.

The 6 MHz with USB Full devices may work in some cases with short cables, and some AVR programmers only use USB low speed anyway - those are less sensitive to this problem.