I put a 6L80e (with its T43) behind an E38 ECM with an OS designed to work with a 4L60e/T42. For the most part, things worked fine, but there was one big bug- the engine would go into reduced power mode every now and then. The problem went away after loading the correct OS into the ECM (one designed for the 6L80e).
A more recent problem I'm having is using a 2007 era OS in the TCM and 2009 OS in the ECM. Some of the message structures must have changed in the two years, because the ECM is not correctly reading the gear selector position from the TCM anymore. No backup lights, no crank relearn (ECM always thinks trans is in D), no idle speed compensation during garage shift, etc.
You'll probably get something that works, but expect some bugs.