Two pieces of glass will just add surfaces and reflections, I think. As for flat film, you may recall
my story a few months ago about making a
serious effort to re-scan one of my favorite slides, the pool with lily pads and the sun reflected on it. I ended up using multiple focus points with the scanner (Vuescan allows placement of focus point) and focus-stacking the resulting multiple scans. It's not something I would do as regular workflow, but I
wanted that image!
The only other thing I can think of would be to use a very small aperture to maximize depth of field, which may not help much anyway, since DOF in macro with tubes seems to be measured in angstroms.....
I've been thinking about trying this method of digitizing, but the effort of cleaning the slides I'm scanning, around 50, even 60 years old, makes the I.C.E. feature in the scanner look really really worthwhile! It works well.... enough. (If I may be permitted a GlaDOS quote from Portal 2.)
EDIT: Thought I'd add some dust filtering to the mix.... This is a slide of my aunt in 1954, actually three years before I was born. She was newly married, and showing off some cooking skills (which she definitely had!!!) Here is the full frame unfiltered and filtered, then a detail of the center with the same comparison.
The filtering is all in the scanner hardware and the software's use of the infrared scan, no other work or cloning to clean anything.
I know this is cruel, because you've said that film scanners are too expensive. Well, they are! This one is refurbished from an eBay vendor, and he warranted it for a year. It was a little over 300 bucks, and when I upgraded to my current PC (No PCI slots and 64-bit Win7) I had to find software (Vuescan) and a PCIe SCSI card. He honored the warranty, too, when the power supply went out on the scanner. Downside to this scanner, it's a SCSI interface, and the cards are not exactly free if you need PCIe, although you can find one for somewhere between 50 and 80 bucks. He supplies a PCI card with it.