Paint the beam and post all over then attach the two. This will have two painted surfaces touching anywhere there is contact. On the plus side there will be no exposed bare wood anywhere, on the negative I somehow have to account for the thickness of the paint in cutting the lap or have it not quite smooth across the joint.
Since you're planning on using bolts to join this is theoretically an option, but as you say it is difficult to allow for the thickness of the paint layer. And even though this isn't intended to be a glue joint (where a very tight fit is normally vital) ideally you do still want it to be tight for structural reasons.
If you get the fit slightly too tight you'll end up peeling some paint back as you push the parts together; this isn't a problem inside the joint but it can create an ugly roll of paint at the edges which can be difficult to clean up neatly.
paint the beam and post but do my best to not paint the area the beam and post meet.
This is what masking tape is for. Literally :-)
If you worry about having any exposed wood you can cut your masks slightly undersize. Alternatively, you could do any necessary touchups later, using a smallish artist's brush or a Q-tip.
Put it all together then paint. Not ideal as I have to paint it in place...
Honestly I think this is how >95% of people would do it since pre-finishing isn't too common.
and if it is ever moved I am back to number 2's issue (or if it shifts a little over time).
If the joinery is tight enough to begin with there won't be any shift worth noting. The wood may shrink slightly over time but any permanent shrinkage will A) take a long time to occur (possibly decades) and B) could be so slight that it won't make any difference (because the total shrinkage will be so small, due to the dimensions of the pieces). And remember the carriage bolt does auto-align the joint.
given I am a beginner and the lap will be far from perfect anyways
Don't accept defeat before you've even tried ;-)
Lap joints are a great beginner's joint because they are relatively easy to create, and as a result are easy for even novices to achieve a nice tight result... as long as they follow the tips the experts give and take their time. My first half-lap joint, when I had minimal tools and no experience, was tight enough that the two parts had to be squeezed together, because I followed the tips and took it slow.
Just carefully mark out, saw inside your lines, pare carefully with a chisel and don't rush, and you should be able to get a pretty decent result on the first one, and each subsequent lap should as good or better. But by all means practice on some scrap before attempting this on the project pieces if you're hesitant.
