the Zero LiPo only use bcm4 (as a voltage warning that you can assert low). pHAT DAC requires the I2S interface solely - so there are plenty of GPIO leftover.
How you assemble your setup is up to you. Typically you probably would be soldering the Zero LiPo directly to the Pi male header, and use a standard female header for the pHAT, which would leave enough clearance for the LiPo connector.
If you use a stacking header in place of the female header supplied with the pHAT then you’ll get easy access to the (unused) GPIO, though it may be better to just tap into the top of the pHAT DAC to hook up your external components (IR sensor, or whatever you plan).
I’m working on something similar to this actually but have nothing to show right now… still the above should give you a fairly good overview of what is possible?