Noda b'Yehuda on what to do if one leined shekalim before the kriah of rosh chodesh

There is a machlokes Rama/Taz in siman 684 regarding what to do if on rosh chodesh teves/chanukah the tzibur mistakenly started leining the chanukah kriah first instead of the kriah of rosh chodesh, which should come first.  Rama says to stop immediately and switch to reading rosh chodesh.  Taz disagrees and says that even though rosh chodesh is tadir and therefore should come first, tadir is only a lichatchila and is not m’akeiv. 

 This week we have shabbos shekalim and rosh chodesh together.  Noda b’Yehuda (mh”t 11) was asked what to do in this case if the tzibur mistakenly started leining parshas shekalim before the kriah of rosh chodesh.  Lichora this sounds like it should hinge on exactly like the same machlokes Rama and Taz.  However, Noda b’Yehuda says here l’kulei alma you should continue and not stop.  What’s the chiluk between the cases?

In siman 684 there is another din that if you took out only one sefer and read the leining of rosh chodesh and left out chanukah, you are yotzei.  GR”A points you to meg 29b that “ain mashgichim b’chanukah” (which if you look up the gemara you will see means something else in context).  That’s why Rama holds that when you took out both sefarim but started reading the chanukah leining first, you stop right away.  It’s not just that rosh chodesh is tadir – it’s that chanukah really carries no weight compared with r”c.  

The same is not true of shekalim.  If you didn't take out a sefer to lein shekalim and just leined the kriah of rosh chodesh, you haven't fulfilled your chiyuv properly and have to take out a sefer to read shekalim.  Since we see that shelakim does carry at least as much weight as the reading of rosh chodesh, you cannot stop and cut it off in the middle.

(See further in the teshuvah where the Nb"Y discusses which haftarah to read.)

I understand the proof, but I don’t understand the lomdus/sevara.  Why is the leining of chanukah “ain mashgichim bo” viz a viz the kriah of rosh chodesh but not shekalim?   

I am not sure, but my thinking so far is that when it comes to chanukah and rosh chodesh, it is the kedushas ha’yom that gives rise to the chiyuv of kriah.  For whatever reason, the kedushas hayom of rosh chodesh eclipses that of chanukah, and defines that kriah as the primary one of the day.  

Yesh lachkor: do you read parshas shekalim because it’s Shabbos shekalim, or is it Shabbos shekalim because you lein parshas shekalim?   Obviously, it's the latter.  It's not the kedushas ha'yom which is mechsyeiv the kriah, but aderaba, it is the kriah which gives this shabbos its unique name and character.  Therefore, the kriah of r"c which stems from the kedushas ha'yom cannot substitute for or eclipse the kriah of shekalim, which is an independent chovas ha'gavra.

(Yes, I am aware of the Rav's piece in Shiurim l'Zecher Aba Mari about the function of krias haTorah in establishing the kedushas hayom of chagim.)