When power is first applied to the BMU, it assumes all switches are non-functioning until proven functional. So it lights the BMU indicator (big red triangle). If you activate each switch in turn, front then back, the BMU will test that the brake light illuminates with each activation. If it detects both switches illuminated the brake light at least once, the red triangle indicator extinguishes. Thus the BMU is testing three things on the brake circuit:
1. the brake light itself is functional
2. the front brake switch is operational
3. the rear brake switch is operational
Once this one-time first power on test is successful, either brake switch will operate the brake light and the BMU indicator will never light up. From then on until power is lost, the only condition that will cause the BMU indicator to light up will be if the brake light bulb burns out.
Since you bypassed the BMU in your effort to test the rear brake switch, you bypassed this critical power-on test for the rear switch and thus the BMU indicator never went out.
Your problem with the rear brake switch is concentrated around the wiring to the BMU since neither switch passes the power on self test. The assumption is that nothing in the wiring has changed since the rear master was replaced so there's a disconnection somewhere.
Fuse #1 is the only common element between the front and rear brake switches. Have you checked for power on the Green/Black wire on both switches when you first power on the bike?
Have you checked for power at the Grey/Yellow on the rear taillight connector when you activate either brake switch with the power on? Disconnect the brake/tail light from the harness to run this test.
P.S. In this entire thread, I'm assuming that the Skene LED indicator is wired in PARALLEL with the brake/tail light. Is that a correct assumption?