Is there are general rules to align right-aligned elements on the page?
Look at these screenshots:
At this screenshot the search icon and the link are aligned to the right border of the "box", while the table column header and the checkboxes are aligned with some padding from the "box".
At this screenshot I had aligned all the elements with same padding from the box.
Is it right way to do the best design ever?
There is no right or wrong way, design is always subjective and dependent on what you are trying to accomplish. With this in mind however, assuming you want something that looks more uniform, I think the second is the better option.
The reason is that because the text in blue has a lot in common with the element below it (the black text) - it should probably line up with it.
Arguably though, maybe you want that blue text to look 'out of place' and it is your intention to draw the eye to it. In that case the first option may work - just know that it can be visually a bit awkward and it will draw the eye. (This can be a good trick sometimes for call to actions etc)
If you removed the black text, option one probably would be better in my opinion, as the edge of the tables is slightly stronger than the edge created by the checkboxes. Either could work though, as there are no obvious mis-alignments on the page.
I guess, always favoring the strongest established line/edge is a good theory (again, unless you want it to draw the eye)
