In short - yes, but we don't yet know how. Anyway - now you can have as much apps as you want on one card, not just one
It's the reader app that has to be modified. There are two ways:
- the easy (and dangerous) way: integrate the autorun.xml with reader's software the same way the apps are now integrated into the launcher. The drawback is that you'd have to reflash the reader to reconfigure installed apps, and making a mistake in some app can brick the device (Invalid autorun.xml file crashes the device - if that's integrated into main UI...well...you know...KIA

.
- the hard (but potentialy safer) way: figure out the api to load UI from external xml file and integrate this feature into reader's software. This way we can start any app we want and it's safe - in a worst case scenario you'd need to reset the reader. The hard thing is that we don't know it, and knowing it probably requires reverse engineering some part of reader firmware...:/
Anyway, we keep hacking