Alleyways To Torah

I think that this generally touches on the equation between זריעה בשבת to זריעה בכל התורה כולה. It is quite possible that each זריעה is unique and that comparisons cannot be adequately made. מנחת חינוך is מאריך in such ענינים.
To make a long story short (my posts have become unnecessarily long), I have heard Rav Rosensweig shlita suggest in the distant past, in explaining discrepancies in רמב"ם between his formulations in הלכות שבת and those by other types of זריעה, that there are different foci in each context.

For שמיטה ויובל he suggested that the role of קרקע is most crucial (ושבתה הארץ), which is why certain actions that רמב"ם terms מעין האב by שבת become תולדות by שביעית; the focus is harnessing the power of the קרקע to transform and create through the זרע. So while, say, מרכיב aids growth, it doesn't use the קרקע as much and will only be an איסור דרבנן.

Then there's the איסור of אשר לא יעבד בו ולא יזרע by נחל איתן.
רמב"ם in הלכות רוצח says that the איסור is עובד שם עבודה בגופה של קרקע. The difference between this and שביעית, despite that they both relate to the קרקע, is that שביעית is about stimulating the power of the קרקע and having the גברא channel it into the resulting צמיחה שבקרקע; the איסור here is defined as doing the actual עבודה in the גופה של קרקע. This is why, for example, משקה is left out here and why חורש is included here while it does not appear by שביעית.

The last זריעה that was addressed, which he believed was somewhere in between, is כלאים. There exist peculiarities here as well, discrepancies between this, the categories above, and הלכות שבת. In כלאים there's no sharp idea of ושבתה הארץ where it's about enlisting the קרקע in the process of growth, it's simply about the creation of a חפצא של כלאים. This is also distinct from שבת which is clearly much more focused on the גברא doing a specific מעשה (WE are שובת). But the creation of the חפצא here is still connected to the קרקע more so than by שבת, which is why מנכש and מחפה are more prominent here than they are by שבת, where it's much more about the צמיחה.

In terms of שבת itself:
This goes to the heart of the whole issue of השרשה, and whether צמיחה and כוונת זריעה are מעכב.
מנחת חינוך thinks that it's completely מעשה-oriented and one will be חייב immediately, even if one's כוונה is זורע על מנת לעקור. He says that השרשה is important by כלאים and שביעית because they are more about מחובר and תלוש, which works well with the above חילוקים.

אגלי טל disagrees, so while he thinks the מעשה זריעה is the focus he thinks that על מנת לעקור won't be זריעה.

רש"ש says that if one puts down the seed and then picks it up later, before השרשה, he'll be פטור.

Obviously זריעה בשבת will be closely related to how one understands בישול. There is much to be said and much was said about these issues.

I hope I have given a possible answer to the question - כלאים is only after השרשה because the איסור is the creation of the חפצא, while by שבת the focus is much more on the actual act that the person in question is proscribed from doing.

Tyere Will

Erudite as always!

See - if you wish - my article in the one and only Netiv Aryeh torah journal where I touch upon [with loads of siyata d'shmaya] this topic. If you enjoy reading the article even 1/100 of how much I enjoyed writing it, you will have a ball.