Hello, MarijnS:
There is no such a tool for processing only inside of an irregular boundary shape, but theres is a workaround that can do something similar. Besides what Olihar suggests that is to srink the bounding box to a size that encloses only what you need, I must agree with anyone complaining about this method not being very cost-effective in many cases where a box shape is not what we want, but rather is a U or an S or a circle shape.
For example lets say you have aligned a full dataset covering an island with round shape and 5km radius, and now you only want an ultra-high quality model of the coast with only 30 metres width without having to spend days processing the interior. In that case you would love to have a way to workaround. Well, here is one.
Right over the sparse cloud draw a polygon enclosing the area that you want (do not try to be super precise), then right clic on the shape and pick filter photos by shape. Then select all photos remaining on the photos pane and then go to the 'Edit' menu to pick 'Invert Selection' so that everything but the the wanted photos become selected (and turn pink)
then right click on the model viewport and use 'disable images' (and deselect all by selecting nothing with the fence tool in the air)
You are now ready to process just the subset of images that matter for the area you wanted and afterwards you will be allowed to use a proper boundary shapes to either clip outside or inside your deliverables.
I hope it helps you and If you wish really to shorten your learning curve from Pix4Death... just let us know.
José MartÃnez & ACCUPIXEL
your Metashape therapists ;-)