Nope. Regardless of a smooth or rifled bore, the basic function is the same. Charge the pistol with powder, and then press a lead ball wrapped in a cloth patch firmly down over the charge. The ball is a bit undersized for the bore, and the cloth patch, makes it a bit oversized for the bore, which results in the ball staying firmly in place through friction. Alternatively, a wad could be rammed over the powder, the loose fitting ball dropped into place, and another wad rammed over that to hold it, although I have rarely read of this practice. Flintlocks are not exactly my forte.

The priming charge would sit in a flat pan, and would be held in place by a tight spring loaded "frizzen" which also serves as the striker for the flint when the gun is cocked and fired. So in a properly loaded, solidly built flintlock, there is no concern about losing the powder or ignition charge.

This is a very interesting question, and one I've never seen specifically addressed. It does not seem to have been a notable problem, perhaps because of the factors to be discussed below.

Muzzle loaded weapons, both pistols and rifles, were loaded by means of a pre-made paper cartridge, or with loose powder and shot. In the case of the former, the remnants of the paper cartridge would be stuffed down the barrel after the powder and shot and tamped firmly in place by means of a ramrod. In the case of the latter, the ball, unless loaded in a hurry (unlikely, given the parameters of your question), would be wrapped with a patch of cloth or leather, for the same purpose as the paper: to secure the (generally undersized) bullet in the base of the barrel, with the powder trapped beneath the bullet. This is easier done in a rifle, where the grooves cut in the inside of the barrel help to hold everything in place; but most pistols, especially those intended for self defense and military usage, were smoothbore.

Due to a variety of reasons, a wise man would be unlikely to leave his pistols loaded for any lengthy period of time. Gunpowder draws moisture to it, and once damp, is either much less effective, or utterly useless. A morning dew can be sufficient to render a weapon inoperable. The best course of action would be to draw the charges, or to discharge the weapon, every morning, or to only load it when in a situation that it might prove necessary: upon setting out on a journey, or on the eve of battle, etc.