I found the antenna mast, part # 86309-48040, for $39.72 at:
http://www.lexus-parts.com/
And no, I haven't removed it yet, mainly because of your concerns. I am supposing those caps can be removed, but I think I will get the part first and see if they have instructions and/or replacements. The sales blurb says: Designed to be user friendly for installation.
A fellow at Sewell lexusparts.com has helped me with this. The amplifier unit needs replacement, plus the mast, and that means removing the headliner, which seems like a lot of work. Once the headliner is off, the amplifier base unit looks to be easy to remove and replace.