Minimum load current from charger IC
The BQ24xxx/BQ25xxx family of PMICs don't have cut/off or shut/down artificial limitations. Unlike the "powerbanks" that must save the battery when no load, these ICs don't disconnect at low current, otherwise their use in mobile devices (as the primary power management and power source) would be a disaster.

I have devices based on BQ24296 and BQ25896 chips, and they don't have any cut-off limits. I am not sure what the ISYS(LOAD) is, the TI tool doesn't seem to have any description nor control bit for this, but the IBAT(LOAD) has a control bit7 in I2C register 03. When activated, the IC drains 16 mA from the connected battery. If not enabled (by default), the battery provides whatever voltage at no load.

The IC has an obvious disconnect when battery voltage drops below certain threshold, which is programmable, and set to 3 V by default.

So, it definitely looks like your concern about battery drop-off in MCU low-power mode is unfounded. The coin-cell backup might be a good idea though.

I think it would be a good idea to open a support case with TI and ask for clarification what these functions are about, or post a question on their discussion forum. At least the search for "Battery discharge load current" yielded no results other than links to the datasheets. It might be that these functions are for power bleeding in case of total system shutdown.