There isn’t a hard-and-fast rule about when to use clear or frosted flame-tip lamps (B10 is the industry name for them). It depends on the type of glass.
If it is translucent, I usually use frosted lamps to keep the illumination even.
If the glass is transparent or clear with a pattern (like water glass or seedy glass), I will use a clear lamp to help project a pattern onto the ceiling or walls.
If it is clear colored glass, I will use a frosted or white opal lamp to give it some visual presence when seen through the glass.
You are right, though; the clear lamps can be glary. Having them on a dimmer or in a lower wattage will help.
There are now some really good LED B10 lamps on the market that have the color temperature of incandescent light and are dimmable. Two of the ones that I have tested and liked are made by Borealis and Archipelago.