Hi Peter,
First of all, if low power, long battery life is your absolute priority, then using the iMX6 for an RTC is not going to be your best approach, external RTC's will provide better battery performance.
The RTC in the iMX6 is part of the SNVS domain, there is other functionality associated with that block (powered from the VDD_SNVS supply). You can minimise the SNVS current draw, refer to the relevant HDG (you don't make mention of the actual iMX6 family member you plan to use) for more details, likewise refer to the datasheet for the minimum VDD_SNVS level.
For your second question, I'm not 100% what you mean, but I think you mean in your application power can be pulled without a controlled shutdown, in which case you should have some sort of low voltage monitor that will generate a reset etc.
As for any potential impact on battery life, I don't believe so, the VDD_SNVS domain is electrically isolated from the other supplies, if/when VDD_HIGH is removed the SNVS domain will switch to the VDD_SNVS supply automatically.
Regards
Ross