Washing your parts in IPA is what ruins the transparency. You can get transparent parts using Ember by skipping the IPA wash and instead curing under UV light in an inert atmosphere. I've done it by piping nitrogen into one of these. The key is that the oxygen level has to be below 50 ppm.
I haven't printed with PEGDA or used silanized glass, but whole point of using PDMS is that it provides an oxygen inhibition zone right above it, which prevents resin from curing onto the window. If you were to use most kinds of glass, pretty much any resin would attach to it the same way it attaches to the build head. If it didn't, all stereolithography printers would use glass, as it's far cheaper, more durable, and easier to deal with than PDMS. But if silanized glass can be used instead, that would be pretty groundbreaking.