I have used the manual installation tool provided by Fairphone once after my Ubuntu Touch porting attempts had failed miserably. And in fact the bootloader was locked after the script had finished.
Not sure if it helps much, but the output of this command looks like “oem 8901_lock” can be performed by the tool:
$ strings FP3_flashall | grep lock
./linux-x86/fastboot oem 8901_lock
./linux-x86/fastboot oem 8901_unlock
Edit: this seems to be somewhat different than “oem lock”, see Device stuck in fastboot mode after oem re-locking