This can be done with some caveats.
Windower loads the plugins and scripts in the folder in which it resides; however, it uses the FFXI settings from the registry and the FFXI installation folder to launch the game.
In short, the benefit to having multiple Windower folders would be to have different init scripts and specific settings, which can be beneficial when launching multiple instances of FFXI with different resoltions. The drawback is you'd have your scripts and plugins in two different locations, which can become a pain to manage and update.
I've considered doing this, but ended up sticking to a single folder installation. Windower can be launched using an alternate .ini file for settings, however, some registry changes need to be made if you're working at different resolutions. I kind of outlined how I do this
in a previous thread... there might be a better way to accomplish what I'm doing, but it works flawlessly for me.
The only thing to keep in mind when using that method is you do not want to launch the 2nd instance of Windower before the first instance is actually in FFXI (past the play button, before the Character Selection screen).
Multiple character compatability: I have a script I run whenever I log into my second character that changes the posistion of on screen elements (Distance plugin, etc.) to adjust to the smaller resolution... I also have it drop down the drawdistance. Because my alt's BLM scripts might different from mine main's, I have separate scripts for those. Spellcast is simple... you can use Charname_Job.xml for files that differ between characters (Tragedie_BLM.xml and Minxie_BLM.xml, for example), or stick with a single type for basic scripts or ones that have identical gear (SMN.xml might cover both chars with identical gearsets, etc.)
I think autoexec supports performing actions when you log in at a certain resolution, so some of the stuff I'm currently doing manually (out of habit and laziness) can probably be done automatically.
What is the main thing you're trying to accomplish with two Windower folders?
On a side note, check out FFXIAH's new
Windower Support Section. Don't know if a mod can move this thread, but I think it's a good question to have listed there.