The issue is, that unless you have the Professional version, we can't enter references, control points, markers, so MS can't know which way is up for whatever object you scan... Tho i think if your imagagery is from a drone, i think it does takes its orientations info from the pics? Correct???
Anyhoo...
I've made a Feature Request asking for a very basic referencing system that'll allow us to place at least 3 markers, control points down, which then allows us to correctly set the orientation and scale of the model. There's so much to MS Pro's referencing system it seems, that the subset i'm requesting shouldn't tread on the toes of the Pro version, and it's use in the industries that demand very high level of georeferencing, etc...
Having 3 or 4 basic xyz control points would just make everything really easy...
All i do after alignment is to rotate the model relative to the grid, in ortho view (5), pressing 1, 3, 7 to get the views from the top front and sides (ignore the left/right, they're actually the other way around, but it doesn't matter really).
I then scale it to the grid (set grid to 5m in Prefs), using features i know the distance of.
Then rotate and resize the region to match the model. The ball, etc then aligns with the z-up of the model.
For me, the trackball is just waaay to small, so it makes rotating the model around really twitchy and cumbersome, compared to what i was use to with good ol' CATIA V4, that i once used a lot.
So yeah, Metashape could do with some work on the 3D navigation... And if we had a choice of styles in the Preferences, with a parameter or two when required, it'd just keep everyone happy, and each user would get that bit more out of MS... Helping MS sell more copies.