The current implementation of org-timer-set-timer calls org-notify with the PLAY-SOUND argument set to 't', which gets passed to org-clock-play-sound that then in turn calls the beep function. The value of this argument should be defined in a defvar so as to allow the user to modify or dynamically set its value. Additionally, a similar behaviour should be allowed for the message by having the first cond case, in the cond that sets hl, return the value of a defvar should that defvar be a string type.
Sincerely, Devin