It wouldn't be usual in my opinion to 'seal' any gaps between the floor and skirtings or kickboards... the skirtings or kickboards should have been installed very closely to the floor, and any remaining gaps would usually be left.
Caulk is just different to silicone.. perhaps it's an acrylic compund but it'll be more complex than that.. .
First Google result
http://www.wisegeek.com/what-are-the-different-types-of-caulk.htm
There are also mixes of caulk and silicone in the one tube.. this can be used anywhere you can use caulk, but not as a replacement for silicone.
Silicone is used to produce waterproof seals.. in kitchens and bathrooms. Some tubes of silicone have anti-bacterial and anti-fungal stuff inside for use in bathrooms.
Caulk is used to fill gaps between furniture and walls for example, or around door frames, or along the top edge of badly fitted skirtings.
There are other things in those tubes (mastic tubes)... like waterproof sealent, for sealing around the outside of windows, or whereever... these might be neither caulk nor silicone but it doesn't really matter what the stuff is as long as it works in the way you want it to.
You can use any of the above really... if the colour is ok... but as I say, I don't think gaps like you describe should be filled unless you have to... and it appears as if you have to if there's an unexplained 6mm gap. Caulk would be the most suitable.. silicone is too sticky and messy, you don't need it's waterproofing qualities... and obviously more expensive weather sealent is un-necessary.
Just try a paint shop who should have many colours.