No, the MXI-3 connection will not connect the two chassis's RTSI lines together. However, you can take advantage of the PFI lines on two of the DAQ boards to output/input these signals between chassis.
In fact, here is an example program that demonstrates synchronizing two boards using the PFI lines.
Synchronize Two E Series Boards Using PFI or RTSI:
http://venus.ni.com/stage/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3E61156A4E034080020E74861&p_node=DZ52336&p_submitted=N&p_rank=&p_answer=&p_source=Internal
I hope this helps!
-Russell
Applications Engineer
National Instruments
httP://www.ni.com/support