The calendars found in Tools/ChangeWorkingTime are where you define the
hours of work, the so-called "base calendars." You pick one of these to
serve as the Project Calendar, essentially the description of the default
working times.
To undertand the Tools/Options settings, first understand that ALL date
fields are actually date/time field, regardless of whether a date format is
chosen where times are displayed or not. When you manually type an entry
into a "start" field but do not actually type the time, Project must make an
assumption as to what time you mean. That assumption is defined by the
"Default Start Time" (or "Default End Time") entries. IMHO these should
normally agree with the start and end of your workday but there's nothing
that says they must agree. It's especially important to note the setting
them DOES NOT change the working time calendar.
Likewise the "Hours per Day", "Hours per Week", and "Days per Month"
settings. Durations are stored and computed in minutes. When you enter a
duration in some other unit - let's say "3 days" - Project must convert that
into minutes for storage and processing. Likewise when it displays
duration - say, in the Gantt chart task table - it must convert back from
minutes which it's been using internally into the units you prefer to see.
Those three settings are the conversion factors it applies to make the
transformation. Again, they usually should agree with the length of your
normal workday and workweek but there's nothing written in stone that says
they must always agree. Most importantly, changing them DOES NOT change the
length of the workday as reflected by the start and finish times in the
Project calendar.
In fact, nothing on that page changes ANYTHING in any of the calendars used
to schedule the project's tasks.