Based on Dot4 brake being a hygroscopic fluid (water absorbing vs Dot5 being silicone and not water absorbent), I would think that would not be good in the fairly 'open' area inside a dust seal vs the enclosed area of a piston seal that is already directly exposed to brake fluid on the inside. The dust seal keeps the slider pins from getting dirty, rusting and/or gumming up by the silicone grease displacing space inside the seal where moist air could rust the pin and also helps the boot stay pliable so it can do it's job of keeping direct moisture out.
Likewise, using silicone grease during the assembling of caliper piston seal is a big no-no, citing glycol brake fluid contamination issues.
My $0.02 anyway...after a little internet search.
Bolded comments on dust seal. How do your slider pins look? Those are the ones protected by the dust seals (if I recall correctly) and are what the silicone grease is protecting/lubricating, as well as keeping the seals themselves from drying out and cracking.
Unbolded comments, I reread...you're talking about the piston dust seals, not the slider dust seals...I'll go back to my corner now! Am going to my parts bin to see if I have any dust seals on hand. But would concur with the same principle, since the dust seals don't come in contact w/ the brake fluid, I'd use silicone on them. I would think the combination of the piston seals and dust seals would prevent any cross contamination especially with as little movement as the pistons have between applications and between new/old pads. The separation between the two seals is probably greater than any travel other than initially being pushed back into the caliper. But I will defer to others who are more brake savvy than I obviously am, and welcome their answers!
Looked at my service manual (2003-2005, pg 17-36 and figure on 17-35), the reference to 'open ends' refers to the pistons themselves:
Coat the new piston seals with clean brake fluid.
Coat the new dust seals with silicone grease.
Install the piston and dust seal into the grove of the caliper body.
Coat the caliper pistons with clean brake fluid and install them into the caliper cylinder with their open ends toward the pad.
Is that what you're asking and maybe confusing that statement with the dust seal itself in your last sentence in Post #3?