When the speaker says 坐下來, it is very likely that:
1. the speaker is sitting himself and he would like the addressee to come sit with him(the speaker).
2. if the speaker is not sitting down, then it's possible that they are in the speaker's house and when he asks the addressee to sit with him, he means to invite him to sit within the house (the speaker represents the house)-->he invites the addressee to sit and stay with him in the place. This is similar to the use of 留下來吧！=Stay!
When the speaker says 坐下去,
1. it sounds as if the speaker is giving a command, and the addressee is not told to sit down so that he can be seated "with" the speaker. It sounds harsh, so sometimes we would use only 坐下
2. another use for the suffix -下去 would be to show determination. It means that you can take the action only if you have determination or firm will. It describe a decisive and prompt action. Some examples:
A: 這個東西給你吃一口，很健康！ Take a bite of this, it's healthy!
B: 這個我吃過，超難吃的！I've tasted this before; it is gross!
A: 但是很健康，你吃一口吧！ But it's healthy, just take a bite!
B: 呃... Uh...
A: 你就吃下去吧！ Just eat it!
A: 我想要報名那個課程，但是有點怕會... I want to apply for that course, but I'm afraid I would...
B: 你就報下去吧，又不會怎樣。 Just apply! It won't hurt!
As to 坐下去, said someone wants to sit down on the grass but he's afraid if the soil would stain his trousers or something. You might tell him, 你就坐下去吧，一點點土不會怎樣！Just sit down; a little dirt is no big deal!
3. a more common one for the use of 坐下去, is to mean "continue/keep on sitting." 你再這樣做下去，屁股會變得更大！ If you keep on sitting like this, you'll get an even bigger ass!
Messquito, you haven't consider the situations when the subject is not 你, but 他. The speaker would just be a narrator in those cases.
Your rules can't apply to these then...