Without knowing details of MOTU's implementation it is hard to answer those questions.
The stream format is not a problem in general, as compatibility can be checked quickly: it either works or doesn't work. RME devices support the stream format that MOTU uses in addition to the newer AAF stream format. This will not be removed anytime soon, even with MILAN certification. And yes, every stream can have a different format (and it can even have its own independent sampling rate).
The issues you'll be facing are more related to the way streams are established in the beginning and how they are monitored. MILAN has a very specific approach to that and it is different from MOTU's approach. I was able, for example, to receive AM824 streams from a MOTU device in a quick test, but MOTU would not receive a stream from the AVB Tool with current firmware (even though it was the same stream format). And as soon as you face issues like that, we can't really help much.
The Digiface AVB has a 'leftover' compatibility mode to provide better support for non-MILAN compliant devices that apparently improves (did a brief test) connections to/from MOTU devices, but that mode applies to all streams (it is a global setting), and then causes MILAN-connections not to function. This mode is not available on the AVB Tool, because it breaks MILAN connectivity and compliance.
The obvious (and probably only) way for manufacturers to be interoperable on AVB networks is to use MILAN (an open subset of the open AVB set of standards). Connecting two MILAN devices will always work no matter what.
For an audio interface like the Digiface AVB, the certification is a bit more complex and this is not currently on our timeline. Think for example about setting the sampling rate over network from an AVB controller while your DAW has requested a specific sampling rate via ASIO/CoreAudio. There are some conflicts of interest where the audio interface has to restrict its configuration options from the network in order not to cause instability in the audio driver architecture of the DAW. But we do test against MILAN devices and make sure that there are no issues that would cause interoperability issues. The Digiface AVB has received numerous firmware and driver updates to extend compatibility in the past year, so generally speaking, it is supported as a MILAN endpoint.