PDFs can be annotated like any other supported file format on the Kindle. PDFs by definition are NOT reflowable, however. It is a fixed, final-view format chiefly meant to look the same no matter where you view it.
You can, however, zoom in. Personally, I am not impressed by the zoom options on anything but a tablet/PC. (Based purely on experience with a Kindle, plus hearsay on MobileRead about others' Kobos.) But that's probably just me being opinionated.
Sideloaded books on my Kindle Touch appear in the main library view, however they have the "Personal Document" banner on the bottom of the cover, cutting of the last portion. That is easily fixed in calibre though. Go to Preferences ==> Conversion ==> Output Options ==> MOBI Output and set the box titled Personal Doc tag to: "
[EBOK]" instead of: "
[PDOC]". Now all books, when sent, will have the ebok tag set.