If I remember correctly from what I read on another forum (can't find the thread now), this protection is active when the system is set up for a compact chainring combination. If you set it up for 53/39, it should work fine even if you are actually running a compact, while allowing you to shift into small-small. Does this make any sense to you? I don't have any personal experience with setting up Di2 so I may have misunderstood what the deal was.
Your theory about chain tension does seem correct, since it is exactly what they to for MTB Di2:
http://productinfo.shimano.com/#/spe...r%20Derailleur (quote:
The DI2 system limits cross chain to prevent a chain from getting loose.).