Hi,
1 - yes
2 - no, well you can if it makes you feel better but it will have no impact on wee_reports other than you possibly removing something that wee_reports or its dependencies require. wee_reports loads a minimal dummy engine that essentially does nothing so its not going to upset a running WeeWX instance.
3 - yes if you want your wee_reports output to go elsewhere, eg not overwrite your running WeeWX instance output if WeeWX and wee_reports are going to generate some common output.
You might be able to use day/month/year/week substitution in your template name to automatically generate a uniquely named file, depends on exactly what you are doing. In any case, if your template file name includes YYYY, MM, DD or WW they will be replaced with four digit year, two digit month, two digit day of month and two digit week of year number in the resulting file name, eg my_templateYYYY.txt.tmpl would result in my_template2021.txt being produced. No guarantees as I have not used this with wee_reports but I don't see why it won't work.
timestamp is a standard Unix epoch timestamp, eg 1633055346
Gary