Oops, my first answer was wrong!
All of the various controls and settings marked "bypass" are only useful on receive, and only bypass the receive preselection aka bandpass filters.
The transmit LPF filters can't be bypassed. However, not to worry. The 6M LPF cuts off well above 40MHz, of course, and it is automatically selected when the transmit VFO frequency is between 35.6 and 61.44 MHz (assuming the default settings have not been changed in Thetis). Unfortunately I don't think anyone has measured filter response curves for the LPF's, so there's no exact data on them.
Remember that all of the BFP and LPF filters are hardware and are not programmable. The frequency ranges shown in setup merely reflect when each is chosen.