CBA Patrols might work IF the units are currently unprofiled when given the order. It's possible that if they have waypoints it still might not work.

Move and Cycle are the only ones that work with the virtual side of things, if a group is spawned into the gameworld, any waypoint type works (can be observed using the operations tablet from the C2ISTAR module).

They will not work on virtualized units, correct. When moving in the virtual world, profiles will move at a speed relative to the speed of the leader of the group (refer to the Virtual AI System module for setting the speed of profiles).

Here's where it gets kind of complicated. If a profiled group has a set of waypoints, with the behavior of those waypoints set to "safe" and "limited", then they will switch to those behaviors when being transferred from the virtual to physical world. This is why if they are in a combat state, there might be combat nearby (something alerted them).

Any waypoint types that are different from "MOVE" and "CYCLE" will work in the same way as a "MOVE" waypoint when they are profiled and start moving in the virtual world.
If you place a group in the editor, give them waypoints, and then profile them (the group) by syncing them to the Virtual AI System module (depending on settings), their waypoints should work fine when they get transferred to virtual world. I haven't actually looked at it, but I believe if you give a group waypoints while they are spawned in, those waypoints will persist into the virtual world as well(following above rules).

You can also take the logic hash that the group is tied to and give them a profiled waypoint which will work whether they are currently virtualized or not, but that's a bit more complicated :)

Explanation was a bit lengthy and all over the place but hopefully it helped to some degree.

Edit: Maybe a small tl;dr will help

"MOVE" and "CYCLE" are the only waypoint types that work in both the physical and virtual world of ALiVE. Profiles are basically a ball of "logic" tied to each group spawned by ALiVE. Inside the ball of code, there is a section specified as the groups waypoints. These waypoints tend to take precedence over any waypoints you try to give the group using standard addWaypoint. This may be the reason your attempt to set the group to "Safe" and "Limited" may have failed.
I'm trying to setup some easy to use (relative) functions to help make it easier to script around ALiVE and giving groups waypoints mid mission may be something to touch on (although it's not too hard once you understand it).

Also take all of this with a grain of salt, mostly just observations and experiences after working with the whole system.

^ great explanation