You're right about the mountain being frequently misspelled. The Topozone map (and I suspect therefore the USGS map) shows "Thompson", Beckey's second edition (1987) shows "Thompson" (I don't know about the latest edition). There seems to have been some confusion on this over the years, but apparently everyone else agrees on the elevation of Mt. Thomson - Beckey and the USGS both show the elevation at 6554' (1998m). :-)
From the point where the PCT passes next to Ridge Lake (about 6 miles from TH), you will be able to see quite a bit of the north-bound trail (the trail loses some elevation immediately after the lake). Two "notches" or low points will also be visible above the trail. Bumblebee Notch or Pass is the first of these two. It is approximately 0.25 miles north of Ridge Lake (the book calls it 0.5 mile but it's less than that). The steep 3rd class dirt/loose rock climbers' trail up to Bumblebee follows a dry wash on its right side. It is the first place you'll see after passing the lake that looks like a reasonable scramble.
I don't see how shortcut #2 could work. There is no boot track heading down to the Commonwealth Creek. We bushwhacked up and climbers left and it was awful, dangerous bushwhacking and 4-5th class loose veggie cliffs before we finally got to the trail again. If you are going back to Commonwealth Creek, why wouldn’t you just take the commonwealth Creek trail?
It's been more than 10 years but this is the way I went with my party. I don't recall it being that bad, by Western Cascades standards.