OK, sorry. I've missed that you refer to the new files as well. For new files the settings for upload should apply.
You are totally right about that, but do those settings you can set there also apply for new files?
It would be very handy if Transfer -> Upload options -> Set permissions would also apply for new files/directories that you create by simply rightclicking in the remote folder and selecting new -> ....
In the current state you have to manually set these permissions or first create the item locally and then transfer it to the remote location.
We would very much like this feature as we work in a large multi user development group where we use permission 2664 so every developer can edit files that somebody else created. Now sometimes people forget to set the correct permissions (mostly because they are used to the fact that right are set automaticly when uploading) and people would have to ask me or the person who created that item to correct the persmissions to be able to edit that item.