The "i removed this with no problems" should be a clue!!
- silicone sealant is not near gnarly enough for the transportation industry - you need Vulkem
or other similar urethane based caulks. Also - others here use self leveling SikaFlex 221 (grey) for small seams but I admire the Vulkem-Tremco product (so far).
For general over coating of gasketed seams Acryl-R or Alcoa Gutterseal - I've used the Alcoa product and have proved to myself it weathers nicely but is a one-chance application, ooze it on in a fine bead and it instantly skims over so you have to wait for full cure to touch-up..