If the author of FC.COM could be persuaded to do so, yes. But given the fact you need a disk to hold the VBXE core binaries, it doesn't seem a major inconvenience to first load the flashing tool from the same disk (although if you're simply switching between existing cores, I guess this does not apply).
That is pretty much the scenario I am envisioning FJC--being inside SDX, say and deciding you want the next boot up to be with the FX core without Rambo emulation (so a base 130XE in my case possessing its inherent bank-switching). Then using FC.COM to switch to this config and reboot and away you go.
I guess copying FC.COM to a 'Tools' or 'UTILS' folder is not the biggest deal in the world. but given SDX has that space set aside for the user to customize it seems a real shame ii just is too large to be written there.
Was it 'Electron' who wrote the app?