How do I correctly power a USB 2.0 while decoupled from signal?
Yes, your second schematics is correct, should cause no problem.

However, the remark about "start of frame" is not entirely correct. Start of frames are differential signals in FS and HS modes, and only LS "keep-it-alive" strobe is single-ended. However, the reference to ground is important when CONNECTING and disconnecting a USB device. Depending on which (D+ or D-) line goes to +3.3V at connect, the host determines if this is a FS or LS device, and acts correspondingly. If the connection goes via FS path, HS chirping protocol gets started. Therefore, you must maintain the reference to ground plane across all USB ports.

ADDITION: there could be only one issue. In USB, VBUS from host port is serving dual function - it also gives a logical signal to device that the port is connected, and it is time for connect handshake protocol. If you permanently supply VBUS to your device, it will think that it is always connected, and will pull D+ (or D-) high, regardless if the host is ready or not to accept it and start the connect handshake protocol. Some older USB hosts can be confused in this situation (connect signal is received BEFORE the port is initialized by host software), and hangs. To avoid this situation, you should connect the cable first to already active host, then plug the auxiliary power.