alpine connections to gmos 04

I am installing a Alpine 9835 using a GMOS-04 into a 03 Yukon XL with Bose System. The directions for 9835 indicate to connect yellow 12volt directly to battery (The label says due to high current draw of HU)and the GMOS-04 indicate to connect 12volt yellow to 12volt yellow. I always did this in the past with these Alpine HU with other harnesses that did not indicate to go through them but this GMOS-04 is the first time I have seen it instruct to wire through the harness.  Here are my choices:

1. Follow instructions of GMOS-04 or 2. Tap the connected yellow wires to the battery thus accomplishing both instructions . I fear this may be too much input through the GM system with onstar chimes etc. and don't want to "smoke anything. I have also had other installers say they always ignored the Alpine directions to. (?)

Any advise appreciated

Also I am concerned/curious about the use of the factory amp as I add a subwoofer to this radio. The setup with the GMOS-04 will retain the factory amp systemcomplete with front stage and subs yet Metra indicates that a sub can be added off the aftermarket sub output by providing separate power. Does this mean there will be two sub systems?