Design considerations for low-current SMPS application
Forget about EMI. Unless you do a terrible job on the layout, you will not have radiated emissions problems from your DC-DC converter. The way I see it, the tradeoff is cost vs battery life. If the battery life is OK, I would stick with the LDO for greater simplicity, interchangeability and lower cost. Also note that the efficiency calculation should not be done at 4.2V, but at 3.7V (the average). So it is 2.5/3.7 = 67%. Quiescent current will also probably be lower with the LDO. Quiescent current may dominate your battery life, if the product will spend most of its time in standby. A simple SOT-23 LDO should handle the required current easily. These are available from many vendors with similar/same pinouts, so you won't be single-sourced (make sure to choose an easily crossable part).

If you do go to a switcher, try to find one that is pin compatible across multiple vendors. These are slightly less interchangeable than LDO's, but you should be able to easily produce a layout that accommodates multiple DC-DC converters. I believe quite a few small buck converters will automatically go into LDO mode at low load (rather than skip-pulse mode). So you might not need to worry about skip pulse anyway.

Do not use proprietary parts that are not compatible with parts from other vendors. You will regret it later when lead time goes to 26 weeks, and you are single-sourced for that part.