There are alternatives, actually it would not be necessary to initiate flashing, just to push APE in and make it happy to keep up the connection, which by default means the flasher program stays active on the computer.
I actually made a special bootkernel that does the same thing without requiring the aid of flasher by ripping the rootFS out of APE and beating it into the right form (my intention here is to integrate ithe BME charging logic into ubiboot, but unfortunately I have not had time to complete that yet...)