I'm I right in assuming that if with a new engine it peaks up to 6500 rpm after start-up, then slows to 6200 rpm when it warms up that:

1 It's not broken in fully.

2 That when it is broken in fully it will peak at 6500 rpm.

#1. Has to do with temperature nothing to do with stage of break in. As an engine gets hotter you loose power. From my expierence 200 rpms or so is typical loss... if you are loosing a lot then you need to look at your baffling. The better baffling you have the better your engine will run and often the longer it will last - especially if you are running it too hot.

#2. As your engine breaks in you will see in increase in power as the rings seat and everything loosens up... how much is hard to say.. couple hundred rpms or so

I am with Sinergy.
Two strokes typically provide best power when not yet up to working temperature. so a (10% !!) power loss in air cooled engines when warm is about normal.
This warming up takes about 2 to 3 minutes. Good cooling reduces the loss to a much smaller amount, so the statement seems to be true, that sagging engines are deprived of cooling. Especially so, if the engine is set up a little rich, such that it slowly rises to best power. If an engine set up this way sags in power, it is an alarm phase one!
An engine that is set up lean, will start sagging within a few seconds.
Apart from that, an engine not run in yet, or a tight engine, will not hold full power. The power loss of these engines will occur within less than two minutes, and progress from slight to worse. This calls for immediate action like closing the throttle in order to reduce the load. Failure to do so will lead to progressive friction heat build up and subsequent damage. That is why during the running in, no prolonged full power, or any power level that the engine will not hold, should be asked for.

I have an engine (Brison 3.2) that runs great with a nice smooth low idle (1650 to 1750) rpm. This idle is still the same after a few minutes of warmup, However, after a 10 minute flight the idle speed increases by about 300 rpm. What is this telling me?

That your idle needle is slightly lean. Starting will improve with richer settings, and idle rpm can be lowered to at least 1500. The downside is that the midrange becomes richer as well and will run not as smooth, though engine acceleration will improve over the whole rpm range. Final adjustment depends on how you fly, and what you need to be happy.

Every twostroke that I have worked with does this. The crankcase will stay cool long after the cylinder is up to operating temp. Once the bottom half of the engine gets hot power drops noticably.

that is complete thermal soak -and all do it -- this takes time but ideally the case never get "hot" like the cylinder main reason is incoming fuel air mix should control heat
after the engine sets at rest , this heat does increase.
aluminum really transfers heat rapidily

yeah baby get that needle correct so life will stay sweet