The uBitx does transmit out of ham bands but the change of filters is set in relation to ham band edges.
Example for 40m, the 7-10Mhz filter is switched ON when the frequency is set above 7,000,000Hz.
At or below that value the 3.5-5Mhz filter is ON. Therefore the available power at the antenna connection below 7,000,000Hz will be significantly reduced.
Although it is possible that an issue exist in the 7-10Mhz filter I suspect more likely an issue with the antenna.
Do you have or can you make a dummy load (example 20 x 1k ohms 1/4 watt resistors in parallel would give 50 ohms at 5 watts dissipation, usable with short burst of CW power to test the swr and confirm a very low swr on the 40m band)?
Regarding the whining, based on your "touch" test on the 25mhz crystal I strongly suspect a Nano oscillator issue. Changing the Nano fixed that issue in my rig.