That's exactly what I've set since years: I have two XWP startup folders with different start behavior. On their first properties page, under the 'Startup' tab, there exist the setting:
Start folder content
(o) Reboots only
( ) Every Desktop restart
BTW: To disable all XWP startup folders once, you can use the panic dialog. It opens by keeping Sh pressed while the WPS starts, AFAIR.