How does the second line jive with af al pi shelo lishma, shemitoch shelo lishma, bah lishma?
I don't know the answer to that but I think he was speaking in the short term like our friend in the article i.e. someone who is trying to keep the shabbos but has no appreciation for it. Yes in the long term it may bring him to even enjoy it but in the short term it is torture.
(Someone told me on shabbos that he knows someone who says that they are not shomer shabbos but they are zocher shabbos

.)
CMIIW but I think that is specifically about Talmud Torah.
The gemara that JJ1000 quoted does mention specifically torah and motzvos but the rambam in hilchos talmud torah 3:5 and again in hilchos teshuva 10:5 only mentions torah and not mitzvos.
I actually seemed to remember that it applied to both. I remember a pshat which seemingly applies to Talmud Torah, hence my "CIIMW".
Correct!
In the famous introduction of the eglai tal - where he writes that Torah is meant to be learnt with a geshmak and if you don't you are missing an integral part of the mitzvah- he makes a pshetal out of the fact that the Rambam only mentions torah nad not other mitzvos.