I was not exactly clear about what is the difference between the two options ? Are you planning to avoid the regulator in the second case ? If that is the case, having the regulator could be helpful for applications where a constant supply is critical( may be an ADC using VDD as reference). Also isolation and protection will also come in picture. If the specs are within the device tolerance, you can use it directly too.
I don't understand why you don't drive the CYBLE-012011-00 directly from the battery. The part is capable all the way to VDD=5.5V.
If you want to supply 1.8V it sounds like you will need a LDO analog VREG as an output. Sadly as you pointed out, there is current consumption usually in the range of 1 to 20 uA even if the CYBLE-012011-00 is in low power mode.
I think you would be more power efficient running the CYBLE-012011-00 at about 5V nominal (during charging the NCR18650PF might see 4.4V). At VDD=5V, the CYBLE-012011-00 in very low power mode should be > 10uA. Besides starting with a higher VDD allows you to set a Brownout voltage detect to a reasonable value to allow you to shutdown better should you need to.