You can tell the software that your nozzle is smaller than it actually is and adjust the filament thread to smaller size, that way it
will slice properly and it might even print what you need. This worked for me on my MakerGear M2 but your results may not be the same.
That feature is already available in S3D, stop printing at so and so layer and start at the next layer with a different profile.
It is explained somewhere here in this forum but you'll have to search as I don't remember right now. Sorry.
I also have first layer and top layer issues using auto extrusion, I can compensate somewhat by using the extrusion jog control and force over extrusion but this is an inelegant and awkward solution and requires one to be present to adjust. As jd_3d has stated they are working on a fix for the next ...
You are starting your prints with your nozzle to close to the hbp, adjust the z-stop to somewhere between .2 to .1mm nozzle to bed depending on your layer thickness you have set. If you use blue painters tape you have to adjust for that also, manually or with z-offsets in the g-code settings area.