I hear what you are saying, but again I caution that you do not rationalize to support what you want to believe.
At this point I am trying to standardize my digitization process and I am thinking a printer designed for printing negatives would make this easier.
You have it in mind that incorporating this in one single machine will simplify the procedure. So let's look at your procedure...
A flatbed scanner uses a bulb alongside the scanning CCDs to measure light reflected of the surface of the item being scanned. Before each scan the CCDs are calibrated to this reflected light, the exposure is set to the light reflected by the bulb. You cannot switch this off, you cannot subtract this or it's effect on the scan.
Now I will assume that you are like me in that when I began I had in no way *standardized* my process and therefore the density of the negatives was a little random...
Basically I lay the negative on the platen, cover it with a glass plate to hold it flat, mask of the remainder of the platen with black cardboard, then leave the top open and use a deck lamp to shine through the negative when I scan. I adjust the density with sheets of white paper between the lamp and the scanner.
So each scan is hardly a *one button* solution. And given that you scan in at a set dpi I'm assuming that it isn't really a *copy* function but using the scanner part to scan then sending to the printer part, (once you have the correct number of sheets of paper). You are ending up with a relatively involved process that includes taking you hardware apart and a *suck it and see* level of calibration, (the scanner always calibrates to the reflective bulb and never to transparency bulb). I'm also assuming that your process confuses any attempt by the scanner to *auto-select* the area to be scanned and so therefore you are going through a preview and select process...
Why do you need the solution to be one single machine, is it the idea that a single machine is a single solution? You're not going to find a simple solution to scanning 5"x 4" negatives in a single piece of hardware. That sort of solution will not exist. Most people don't use 5"x 4" for convenience but for quality and tonality. If they want a *one touch* one quality then they would be shooting 35mm and MF. I'm guessing that you approach the problem as though you're using two machines controlled by the computer anyway, so why not look for a software solution rather than trying to force it to exist as a single piece of hardware?
The EPSON V800Photo has a little button on the front that can be used with utility software and a separate printer to create a *simple* solution. I don't use it so have never loaded it on my computer and so will not know how it works with 5"x 4", but it is configured to allow you to select film negatives as a source in a simple window that pops up on your screen.
Even if this is not the case, with the automation available it's easy enough to scan the negative as a negative, (so the scanner will be calibrating and exposing to transmitted light and so will automatically correct the scan to the full range of tones from black to white), and simply printing the untouched file from a single scan.
It sounds a whole lot more consistent, and a whole lot easier, a whole lot more standardized, than the process you have at the moment.



As far as dust goes, regularly clean out the changing bag. It helps to have a blower to clean the dark slides every now and then. But other than that the biggest difference I have found is in using, or having, a soft water source. I find with my present water that using a washing agent is more likely to leave marks than not using it. Also hang the film to dry in a still room where you're not kicking up the dust every few minutes by walking through it. And never assume that you need to hold the negative flat with a sheet of glass.
The other advantage to a proper scanner like the V800Photo is that the glass on the flatbed has been treated to eliminate Newton Rings, it also has a holder that has a sheet of plastic for this very purpose but it is a bit of a dust magnet and so I just lay the negatives straight on the glass shiny side down. I've not had any problems.



EDIT: It is an unavoidable truth that ALL negatives have faults and that they will ALL show scratches, dust and uneven development. Part of the trick with development/printing or development/scanning is to maximise the density range of the negative. If the relatively small changes in density due to uneven development remain relativity small then they become all but invisible. So good process to reduce them in conjunction with a process that is geared to maximise density in the negative makes them invisible.
If you have a thin negative then when scanning you need to expand the contrast to fill the space from black to white. In doing this you also expand the changes in density due to uneven development, they become visible.
Look at a negative laid on a sheet of paper, then hold it up to the light. This is the trouble that the reflective scan, (that your scanner calibrates for), has on the result. That it produces a very flat or thin scan, one with little change in density. And so you have to expand that density and with it any imperfection the scan picks up. On your previous post quite a lot of what the scanner is picking up is the changes in the surface texture, (and it look like changes in density where you warm finger has increased developer action?), which are far more visible under a reflective scan than they ever would be as pure transparencies.
Here is the same neg scanned as both reflective and transparency, and with a negative that has a good range of densities, not a flat one

. The big take-away is the difference in density the scanner records. I must also add that in using the overhead light in conjunction to a scanner calibrated to the reflective light what you are actually doing is increasing the brightness of the shadows, which will make them darker and block when inverted, whilst really flattening the highlights or denser areas because you add some light to the darker reflective reading. And this is what I see in your scans.