http://planetquake.com/polycount/cottages/crazybutcher/code/wkcopykey_121.zip maybe this helps not my script but did a little extension to it, the original author couldnt be reached...
Take the script posted above, and replace "maxFilePath" with ("C:/Documents and Settings/" + sysInfo.username + "/Desktop/") That should save to your desktop instead of the current file folder.
There are some scripts for it, check http://scriptspot.com. I like the screengrab tool in http://xnview.com, lets you drag a marquee for where you want to grab.
You could always write a quick script that gets the current selection, does a Flatten action, then re-selects the original selection. Or was that one of the 5 workarounds?
Aliases make just different sort of troubles IMO. I have a few masks rendered from cryptomate AOV and save them in a folder "renderoutput" which is aliased in SD . Then I do a new version and have to keep previous render . I do a new "renderoutput2" folder and re-aliase SD to this new folder. But since aliases in SD are…