The Song seems to be self contraindication first it says שכרו הרבה מאד your reward is Great and the it says על פי פעלו according to your Action is the reward great or according to your action?
In addition to my other answer, the Lev Elyahu brings down another answer from his grandfather the Maharsham:
The halacha states that if a person is, say, lost in the desert and doesn't know when Shabbos is, he counts seven days and then observes Shabbos. We sing כל מקדש שביעי כראוי לו referring to a person observing Shabbos as it appears to him to be the seventh day, or כל שומר שבת כדת meaning someone that observes the proper 7th day. For each of them שכרו הרבה מאד על פי פעלו because we don't judge based on a set standard, rather איש על מחנהו ואיש על דגלו - we judge each person based on their current מצב.
(and while the text there is not indicative of this, it could be that with this explanation איש על מחנהו ואיש על דגלו can be explained literally: we dont judge them both on the same standard because one person is על מחנהו - "in the camp" - and knows when Shabbos is, and the other is על דגלו - "[resting] on his flag", i.e. in a temporary place/in the wilderness and does not know when the real 7th day is)
You can really start your question off on the fist line:
כל מקדש שביעי כראוי לו כל שומר שבת כדת מחללו
Aren't those two contradictory as well? Are we discussing someone that honors Shabbos "as is fit" or someone that merely abstains from desecrating Shabbos?
Your question is really the answer: we are talking about two different people! The first guy really dose everything he can to honor Shabbos - nice clothing, delicacies, clean house, etc. The second guy dose nothing - he doesn't prepare for Shabbos, his house is a mess, he doesn't cook, he doesn't even change his cloths. All he dose the entire Shabbos is, say, to sleep!
While the second guy didnt desecrate Shabbos per se, his reward is surely much less that the person that treated Shabbos with due respect! Hence, the next two lines: שכרו הרבה מאד - for the first guy, but only על פי פעלו for the second.
Source: Lev Eliyahu Part I, in the name of the Chafetz Chaim (quoted in Ma'asai LaMelech, Ki Sisa note 1)