Exclude folders from upload that are marked as "Excluded"

Hi,

I was wondering if somebody could help me with my thinkiung (if my thinking is wrong or whether I am misunderstanding some conceptions).

Having a node Project within PhpStorm 9.5 (on Mac Yosemite), I mark the folders node_modules and bower_components as "Excluded" (Right-click -> Mark Directory As -> Excluded). At this point they turn red ( at least in the Darcula Theme). And I do this for 2 reasons:
1. to exclude them from PhpStorm's caching
2. to disable any upload to a server

But: Right-clicking them still allows me to upload those folders via FTP to my server.
This is the first point, where I am unsecure in understanding: whether right-clicking them directly or their parent folder (and upload the whole folder) - all the "Excuded" folders will still be uploaded. Is that intended or am I doing something wrong? Or is the Exclude Folder mechanism *only* for excluding folders from local cache?

Next, I try to exclude folders vie tha "Server Settings Dialog" (reading through this: https://www.jetbrains.com/phpstorm/help/excluding-files-and-folders-from-upload-download.html#d75712e297).
But once I go to the "Exclud Paths" tab and try to select one of those "Excluded" folders, I get the error message "Local path [.../bower_components] is out of project". Removing the "Excluded" status from those very folders also leads to a disappearance of that error message.

Could this be a bug? Or what am I misunderstanding here?

(I finally entered the name of those folders in the "Options -> Excluded Items by Name".)

Thanks for your time and help!!!