I guess I'm confused, what is the problem with the Baofeng and the Connection? Is it not shifting right or adding the sub tone? There's nothing special about how the Connection works from a repeater standpoint. There is some weirdness in coverage in and around Boulder, so are you running into the problem of trying to use the RX-only radio for Boulder?
To get this straight, the Colorado Connection in town runs at 145.310 MHz, -0.6 MHz shift and 123. 0Hz tone. So the radio on Mt. Thorodin is listening at 144.610 MHz and expects a 123.0 Hz tone. It transmits on 145.310 and includes a 123.0 Hz tone. This should be your 'normal' programming.
However, in Boulder and surrounding area there is very poor to nonexistent coverage due to the radio shadow. Mt Thorodin is west of Boulder. You can usually hear 145.310 MHz because the repeater is running a liberated GE repeater with a 4-bay folded dipole array. It's a very good station, good power and very even pattern. But the signal you transmit in Boulder (particularly on HTs and mobiles, home stations with towers are often fine) is not as good and beyond the ability of the station to hear. So there is a radio that listens at 145.310 and re-transmits your signal to the Connection. This radio has a 100 Hz tone squelch so that when you're using it you don't break the system by having two radios trying to open the links. This radio has more limited and uneven coverage itself, so only use it if you cannot use the main frequency.
Just store two Denver/Boulder memories for the CCR. One is normal and the other Boulder radio shadow area. Does this present a problem to the Baofeng?
"Why does the U.S. care which flag will be hoisted on a small piece of land thousands of miles away?" -- Ron Paul