I was wondering if there is a general rule of thumb when compareing boat tails to flat base bullets of identical weight and identical charge weight, will there be a speed difference, will the flat base bullets always have the higher muzzle velocity??

None! The only use for a boat tail is after it transitions the sound barrier. It will be more stable at long range. It is of no use at all at normal hunting ranges. Most of the time a flat base will be more accurate.

Any velocity difference will be because of jacket thickness or length of bore ride. Bullet construction only.

The boattail does retain velocity better because it creates less drag as it travels through the air. Thus it will have a flatter trajectory. This is probably a trivial difference out to 300 or 400 yards. Beyond that it will begin to matter.

Flat base bullets are sometimes more accurate than boattail ones, at least in some rifles, and especially at closer distances.

But also notice that present day match bullets are almost always boattails.

As far as your question about muzzle velocity goes, you can't tell until you load both alike and then fire both in the same rifle and chronograph the results.

A boat tail will magnify the effects of any crown irrgularities. They are of no particular value at ranges inside 500.

all good replies but I think boattails actually start showing differences at 400 yards....at least they do in my varmint rifles.

It depends on the distance the transition point from supersonic to subsonic is.