Yes. Parkerizing the chamber and bore will give you problems, namely difficult extraction, and dimensional changes. It will ruin the bore. It can also built up on joints like sight dovetails, recoil blocks, sling swivels, etc. Usually you remove all attachments first. The military phosphate coats over chrome plated bores and chambers because it will not attack the chrome.
Phospating ("parkerizing") puts a thin, porous, but measurabable coating on the raw steel. It will also roughen and give the chamber or bore a texture.
Professional refinishers will always plug the bore and chamber, usually using a rod threaded on both ends inserted into the bore, and sealed with rubber caps, washers, and nuts. Simple plugs can be used at chamber and muzzle, but they can blow out with the heat.
