Are you saying that you did not tighten the nuts once you found the bolts are loose, or did you tighten the nuts and the toilet still rocks?
I don't think that loose nuts alone would cause rocking. It could be that the flange is high. The problem may be the lack of shims.
I would consider pulling the toilet. Check things out, and then maybe use a SaniSeal rather than wax when you put it back together IF the cause of the rocking is not a high flange. There is not space between the flange and the toilet, I would use wax. Wax can be compressed to zero. Saniseal cannot. I think it takes more skill to use wax and not rock the toilet that is subject to rocking before the shims are placed. I expect there is a technique to accomplish that, but it probably takes practice. The Saniseal could maintain its seal through rocking that might occur until shims are in place.
In any case, I would put shims in to make the toilet level and not rock. If I pulled the toilet first, and especially if I used the SaniSeal, I would use a level to level the toilet with the shims. If I did not pull the toilet, I would use shims to keep the toilet in its current state without rocking.
Some people are more sensitive to smells than others. Sensitivity varies including with age, plus if you are used to something, the smell is not noticeable.
I am not a pro, and I have not used a SaniSeal.