We do not rely on ice and water shield to weatherproof our penetrations...it simply isnt necessary if you know how to roof.
In today's roofing market, much of the skilled labor has been replaced by "quick fix" types of products. Ice and water will certainly do the trick, but it is a sad state of affairs.
Do the flashings properly and you needn't worry about the felt turning up, nor IWS.
You have hit one of my pet peeves. There is no more "sheet metal" skills left in the "Roofing and sheet metal" trade. If it can't be butchered together with an off the shelf piece of base flashing and a couple tubes of sealent, it is beyond the skills of 80% of todays roofers. Just a bunch of shingle nailers.This is just not in the roofing trade, it is across the board. The bar of acceptable workmanship keeps getting lowered.