1.Why the initial size is 3MB for PRIMARY file and 1MB for LOG If the documentation clearly says that It should be 8MB for versions above 2016 and 1MB for anything lower (I'm on this category as I'm using 2014)
The initial size is going to be whatever Model is set to, in this case your model is 3 MB. Who knows why, could be a host of reasons which in the end aren't very important to be honest. Set Model to the starting size you'd like for all new databases or specify the size in the create database command/window.
2.I understand that a log file could grow to 2TB maximum but why the Model database says unlimited and the STACK database says limited to 2TB?
They are equivalent, I wouldn't get hung up on this. Most likely the way the GUI is coded, honestly not even worth making a connect item about.
3.Assuming that the actual default size is indeed 3MB and 1MB, why on the disk, I see 2240 KB and 560 KB?
Model is set to autogrow by 1 MB, so it's 2.2 MB right now... I'm going to guess at 2 MB it grew by 1 MB. The size on disk and the metadata sizes aren't going to match up unless you have a database that is completely and utterly devoid of free space. The log has a size it can't be smaller than, which you're at right now.