In winhttrack I use saved option files frequently for complicate cases such as
wiki sites.
There's an inconvenience in using them, when you load them (Preferences->Load
options...) the "base path" of the project is changed, in a way that seems
related to the settings file location but I don't fully understand, it seems
either the documents folder or the user's folder (it is not an information
included in the settings).
This is inconvenient by itself but it leads to half disasters if you don't
know about it and you load the settings after you already selected the base
path (that is in the "Step 2" phase): here you can't control or check the path
anymore, you just find out after the download ends that it has not been saved
where you wanted, and the files are not even saved in a single folder named
after the project as usual, you get for example with the default settings
multiple folders named after the hosts, in addition to hts-cache and the
hts-log all scattered in your documents folder, and you're lucky if nothing
gets overwritten.
I see no reason in any case to change the path after loading new settings so
you should just avoid that.