If you are using etherboot to load Linux, then you probably want Etherboot/32 because Etherboot/16 is a subset. It only loads tagged images. It can load to extended memory if running on a 286 or above. On a 8086/8 loading to extended memory will silently fail.
If you want to make Etherboot/16 ROMs, you need to change the ETHERBOOT variable in src/Config.