Perhaps I can help explain how Revit wants to work. Means and methods to the madness!
From my understanding, Revit Beams "Joins" clean up with other beams best when they are not 3D Snapped to a column. Meaning, if beam is locked to a column instead of a "Level" Revit wants you to do coping instead of mitering. (But there is another trick that another has mentioned on here, where the Beam is zJustified. Top or bottom.)
Lets look at this example of a simple gazebo.
(Part of the Historical Documentation of my timeshare Hurricane Ian destroyed.)
The 4x8 wood beams/girders on the bottom (highlighted in blue) show a start and end attachment type in the properties. There is also a coping distance now that I selected the apply coping (CP) button. (Typically when doing post and beam construction you want coping applied to all connections. But in several instances you need beams mitered and resting on top of a column or some other detail. (the problem)).
The Reference Level is not correct, (Level 0.1) because when drawing the beam with 3d snapping, it was using the set work plane in that 3D View. (Wonder if it would be different if we changed the work plane to Level 1 or some structural level that is set for beam heights. - I'll let you play with that.)

Here you can see the difference - with the 4x8 beams on top (in blue) - when we draw the beam in plan and specify the reference level - typically the level you draw it in - you will see that the structural info is not appearing start and end attachments. The Reference level is also something we are familiar with or intentional to the structural design, the plan used to draw the beams. (Typically I draw using the closest level for the beams so height adjustments are easy calculations, or I create a structural level.)

You will also see that when we click the Beam/Column Join button, we get this result. It works! But as you can see with the 3d snapped beam to column, it is all greyed out. (Perhaps someday this will change to be more fluid.)

So whats the difference...
Well in the bottom beam, with 3D snapping we have to do coping. Where as the top beams its just joined.
Using 3D snapping is good. Means the beam is structurally joined to the column. I think you want this fro structural analysis, if you get into all that.
(Disallow joining beams from other beams and columns may mess with any structural analysis you are doing. I'm guessing it is Not advised, but interested in what a structural engineer may have to say.)
In this image you can see the 1/8" coping applied... Looks OK but could look better.

It is really all about how you need to have the connections. Is it a real application of steel/wood joining steel/wood or is it a rendering job! If it were real, my sizes, position and coping above is not correct - maybe the beam is too thick for the column or we need some hardware supporting the beam to the column at the specified angle with a greater coping distance. A 2x8 with standard nailed construction is all we need, like so! That looks better. You could do a 0" coping distance, but I like to see the shadow in renderings.

So this is nice with 3d snapping to columns. But best get the work plane corrected before drawing, otherwise we're always editing level and height after creating. And use coping to your advantage.
So what about the mitering method - timber construction techniques - can't we do that for any condition?
e.g., if the beams are resting on top of a column structure.
Well sure. Like this... WAIT... something doesn't look correct.

CLEARLY... we have one problem here - FLOATING BEAMS - because I stopped the column short of the underside of beam... WHY did I do that and How do we resolve this?
So... When we bring the column up to the underside of the beam, the beams break up. The mitering is lost and we cant get it back, the column joined the beams.

So this is a problem... I cope the column to each beam with 0" on each... I even try 1/8"... But it still breaks up.
Here I change the height to be 1.25" below the beam @ -5.25", and the beam is -4" . Stays clean but isn't correct. Agree?... of course you all do!

If we raise it up 1/8" more we get this... No Bueno! I try coping everything at 0" or 1/8" but nothing works. Its as if the system thinks there is a default 1" coping for all structural members. Turning off coping does the same.
Very frustrating.

Ultimately, you want to be able to produce something like standard lumber or Mass Timber construction with my examples. Like this image. Where there is hardware between the beam and column. But its not 1.25" thick.

No worries, and sorry its not a quick answer, but there is one right below.
So all my beams were zJustified to the Bottom. Like so. This is causing the column to continually join with the beams.

So if we change it to the top. Like so... Revit works just fine!
YEA! Hope this helps.

PS
So with that all being said, perhaps a structural Engineer can tell me if changing the zJustification for beams messes up any of the structural analysis tools, if columns are not joined to the beams in the program. I imagine it does, from my understanding, if the beams aren't breaking up they are also not joined to the column. Only the beams are joined together.