Although I don't hardly ever see a 454 block, I thought the Gen V and VI's still had blind head bolt holes.

not on 454's,,I made that mistake 12yrs ago when I bought new blocks thinking they were the same as 502's.head bang

Same issue here with 502 block, aluminum heads and stainless marine. The manifolds have already been clearenced. I have extra lower row outside bolts that I have ground off the top of the head. Since aluminum, I feel I need to keep the washer. Other than potentially causing a "rounding" head issue, any problems with this?

No problem as long as you can still get a socket on it and get it torqued properly.
Eddie