First, please note that the URL for ALL of my TiddlyTools addons – including the “timer” related functions – is
https://TiddlyTools.com. The old URL (It's About Time! — TiddlyTools: "Small Tools for Big Ideas!" (tm)) has not been updated in quite a while and is likely to be “retired” soon.
With regard to your specific question: All of the schedule intervals (Once, Monthly, Daily, or day of the week) can also specify a time of day (hours, minutes and seconds). Thus, if you need to have multiple alarms during the day, you can simply create several alarms with different specified times.
If this doesn’t seem to fit your desired usage, please provide more detail as to what you are seeking, and I will think about how (or IF) it can be added to the code.
Note that the code is not simple and has to be extensively tested to try to avoid introducing excessive processing overhead related to its interrupt driven event handling (which occurs once every second whenever your file is open in the browser). Adding extra functionality has the potential to significantly increase this processing overhead, so it must be carefully considered before anything new is added.