Are these toilet bolts installed properly?
The caps come with a washer-type thing that they clip into:


Your toilet clearly does not have these clips. Using silicone is most definitely not the correct way to attach these, so maybe the installer lost the clips or just has never installed a toilet before? 

It's normal to cut the bolts to length, as the length needed depends on the thickness of your floor. The nice way to do this is with a tool that has a cut-off wheel (eg, Dremel), the not-so-nice way is a pair of cutters since it leaves the edges sharp, but if the cap is attached correctly it shouldn't matter.

Here's what it looks like normally (via Handymanhowto), the clips are clear in this case: