I wonder if anyone has tried casting their own LED optics out of epoxy, such as this optical epoxy (pdf), which is advertised as 98% optically clear.
Most general purpose adhesive/composite epoxies are either a yellowish tint, or will soon turn yellow when exposed to sunlight. Obviously since epoxy-cased LEDs were the standard for decades that other products are available- just not sure if they're easy to get.
Some of the Norland Optical UV curing adhesives/epoxies might work better though they are expensive.
Anyhow, my note there is that if you need to machine a mold for an epoxy optic, why not machine a block of acrylic for your optic?
Unfortunately 3D printing doesn't leave that in the model.
Just to put this into a little better perspective, what I'm trying to do, and I'm sure I can't be the only one, is to find some cost-effective way of producing prototype LED optics according to my own designs in small batches, up to say 50 or 100 pieces at a time. The project also includes creating a software tool that will optimize the shape of lenses and/or reflectors with the aid of the Differential Evolution algorithm.
If the objective is to create batch of optics with known qualities, then you need to very accurately reproduce the shapes produced by your calculations. This will be nearly impossible to accomplish by hand, though you will get lucky at times and come close.
Part of what you are paying for when the shop charges $5000 for a mold is their expertise. They will be able to advise you on things like compensating for shrinkage/expansion, getting the part out of the mold, polishing it, etc.