Little nooks and crannies in the system , like the two you describe , are the reason that I always blew the lines with compressed air , before by-passing the tank, ( after draining and re-installing the rod), then by pass & pump A/F. I used 40 psi air pressure for 10 mins. all taps open and working the toilet valve. My RV had to survive temps as low as -40, before I retired and started going south every year.
Also if you have the inlet line off the pump for your A/f pick up tube, blow the line back to the fresh tank, to clear any low spots there too.
If you don't have access to a compressor , then remove the lines in question and drain manually. You can blow the line back to the fresh tank , by mouth if you have to.