After installing the machine and loading plain A4 papers in tray 1 (it only has tray 1 and bypass) I immediately started getting errors on the machine. The start up page would not print because there was no papper in the bypass tray and for some reason it required A4 paper to be loaded both the tray 1 and in the bypass tray. This continued to be the case until I managed to change the report printing setting "Paper supply" to tray 1 instead of the default Auto. Tray 1 really should be A4 PLAIN LEF at the copier, if you change it to anything else, it tends to cause exactly the issue you describe here. Physically it will look like this
And on screen, make sure it is A4 plain white and that the icon matches the portrait orientation just like it is in the tray n the picture above, anything else will cause failures
For regular printing from the computer, anything but explicitly specifying tray 1 for media will not print with the same error as above, the job requires A4 media loaded in both tray 1 and the bypass tray.
This will automagically be fixed via the above, else you will need to change the printing preferences to match whatever you have set that isn't per the above. Since you appear to be using a Mac, this would either have to be done via a preset, or via CUPS, unlike a windows driver where they can be set in a straightforward manner.
What I want the printer to do is only take media from the bypass tray if the bypass tray is loaded and the loaded media fits the print job. In all other cases it should default to tray 1 and print plain A4. I've set the default paper size to A4 and also set "When specified paper is unavailable" to "Print Letter/A4 substitution". Whatever setting I try for the trays I can't get this to work or at least not the throw deacribed above and refuse to print.
This is covered by the above
Also everytime I load plain A4 into the bypass tray with the short side towards the machine ("portrait orientation") the paper jams in the machine. Loading them with the long side towards the machine ("landscape orientation") seems to work though. You have that backwards, Landscape is Short edge feed, Portrait is Long edge feed. The name comes from photography Portrait is how a picture is taken of a person (taller than it is wide), Landscape is for Scenery (Wider than it is tall). See here. It jams because you did it backward, it expects to have to feed 8.27 inches of paper, when it senses paper still there after 8.27 it stops the feed, because it thinks the paper is feeding slower than it should (but in reality there is in fact 11.69 inches of paper to feed). In this case, it doesn't jam, it simply stops feeding, but it declares a jam because it assumes there is one.