Yes, but I do not think it is possible to automatically switch to the right frequency..You beat me to this idea..
One console (PAL or NTSC) loading games using a flashcard outputting HDMI but able to switch base clock frequencies dependant of it you are running NTSC or PAL code - right?
I do know that there are mods that utilize two PIFs (I thought it was the Otaku mod?) to make the N64 region free. One of the PIFs is then an NTSC variant and the other a PAL variant. Based on cart region it then selects the right PIF. I think the way you can make this is that you make a circuit that detects when the wrong PIF is selected (I believe marshallh explains how it would work earlier in this thread). In that case the N64 will not boot. Then it is a matter of switching to the other PIF and you reset the N64 using the circuit so the N64 boots with the correct PIF. In that case you can immediately add switching to the correct base clock frequencies.
The problem with using a flashcard in this case, is that comes with either a PAL CIC or a NTSC CIC, so based on that the frequency will be selected, which will also be what is used for any game that is launched, be it a PAL or NTSC version. In that case, I think the only way to make something like this is by adding a manual switch with which you can select the right frequency and you need to select it before you start your N64.
Considering I am mostly interested in running NTSC games using a flashcard, I think I will just go with only swapping the crystals.
If I said anything that is wrong, do no hesitate to correct me. I am just basing this post on my current knowledge that might be incorrect.