Why don't LiPo charger chips isolate the output during shutdown?
If I'm reading the BQ24295 datasheet correctly, it can actually isolate the load from the battery.  It does this using an internal switch BATFET, which can be commanded through I2C to turn off (see section 8.3.1.2.1 in the datasheet).

  (snippet from the functional diagram on p.14)

p.s. BQ24295 is a curious beast, because it can create a 5V supply for USB OTG from a single cell.