Is it good when you print a single A3 with AcrobatReader?
On the printing of your 2 planes on an A0, Acrobat is probably trying to fit all the entities in the sheet by taking into account the margins of the plotter.
On plotters, there is sometimes the possibility to set the use of extended formats. This reduces margins. Maybe we need to look at that.
Here are 2 links where they talk about multiple pdfs on a sheet:
http://helpx.adobe.com/acrobat/kb/print-multiple-pages-per-sheet.html
http://www.stanford.edu/group/cubberley/node/3603
Or links directly for the scale problem:
print multiple pdf on one sheet scale problem - Google Search
https://www.google.fr/search?q=print+multiple+pdf+on+one+sheet+scale+problem&oq=print+multiple+pdf+on+one+sheet+scale+problem&aqs=chrome..69i57&client=ms-android-samsung&sourceid=chrome-mobile&espv=1&ie=UTF-8
When you say that the A3 is supposed to be 294x420, it is indeed not possible to have the 420 in sheet feed. The sheet's feed margins limit printing. In addition, if you have traced the frame of your cartridge at 297x420, the margins will be taken beyond this frame and therefore the scaling will be all the more important.
The only solution, in my opinion, is to try to switch to sheets of rendered format (which you will cut to the final dimensions) or as @s.b says, you have to print on a roll support. In this case, the tracker will do the job for you!
In any case, it is normal that you do not have the same margins, it depends on the leaf drive systems. Each tracker has its own training management, within a few mm.