If you purchase and install good quality laminate flooring, you should not have to seal it. Generally, it's difficult to seal and may not seal reliably. Some people will use silicone to seal their floors, but its best to ask an expert because of the skill level to complete this job.
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Yes you can, however, ensure that this is the best option before executing. I do this to reinforce the self-stick vinyl tile and laminate flooring in my basement and it works great. I got tired of dropping a knife or something creating a huge gash requiring replacement. The polyurethane layer has protected my floors for years. Occasional reapplication of polyurethane in spots where needed making it look new brand new again versus cutting out and re-sticking a piece of the laminate floor that will never look as good as new...I use the former. There are a lot of nay-sayers out there about polyurethane on vinyl tiles and laminate floors, but I've always had great success.
Floor drain trap can dry out leaving no seal, allowing sewer gases to escape.
Yes. The purpose of the transition is to create a pleasing edge to your flooring without binding it, since a laminate floor is designed to "float" and must not be inhibited in movement. Silicone, instead of a transition piece, will still allow enough movement for expansion and contraction. In fact, even if you do use a transition piece, it's a good practice to run a bead of silicone along the edge to seal out moisture that could creep under your flooring and ruin it.
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If the toilet is sitting solid on the floor, you don't need to. I would use latex instead of silicone because if you should ever have to pull the toilet, it would be much easier. One reason not to seal it down would be if the wax ring should ever fail. You could have a lot of damage to the floor before you noticed the leak.