360 Intake manifold bolt misfit

Engine block has no alignment pins. RTV sealant was used at front and rear. I tried threading in the longer bolt in a few of the holes and it went well with just a 3/8" wrench, no real binding, just felt as a normal snug fit. There appears to be about 3/4" depth of thread in the head and it opens up in to what is probably a water jacket. I may have made this a larger issue than it is, just want to be sure it is sealed. I believe the longer bolts will work. Thanks for your interest and opinions.