To use a very simple moshol hedyot, a mother tells her son to eat breakfast. Her reason for doing so is so that he will have the necessary strength to function properly at school. But as far as the Torah is concerned his ONLY reason for eating breakfast is to be mekayem kibbud eim and do what his mother says.
That would be true if Hashem (in a Midrash) had never told us the whole דירה בתחתונים thing. But obviously Hashem wanted us to know what Mitzvos accomplish, or He wouldn’t have told us.
If he starts making cheshbonos that the reason his mother told him to eat is to give him strength, he is very likely to decide that he has enough strength, or that he will eat later, and the like, and he may not be mekayem kibbud eim.
That would be true if it would be a side reason. But as learning Torah and doing Mitzvos is making a דירה בתחתונים, and a דירה בתחתונים can only be accomplished through learning Torah and doing Mitzvos, the danger isn’t there.