Why don't you just burn frequency and module type into flash with the bootloader. Then rfm69 could read these settings and it wouldn't be necessary to configure them. That would solve the problem until someone burns their own bootloader at which point they likely know what they're doing.
I mean why really should I have to tell a preassembled Moteino which components came with it.
Hmmm, sounds like putting the cart before the horse. The bootloader should be able to read the interface to determine whether its an HW, W, LoRa, and what frequency. HOW that's done is interesting. Sounds like an SC-70 serial rom on the radio module. If this doesn't exist then I'll take credit for inventing it
Looks like Microchip (and probably others) have beat me to it: 24AA01T-I/LT (1K bit in SC-70-5, 2x2mm, $0.19 each).
And, being I2C interface, I'll bet that the pins could be multiplexed with SPI pins so the ROM disappears after booting and configuration.
Tom