The Hi-Lo issue usually means that the two flanges aren't correctly phased when the spokes go to the rim. Take a look at the 2 heads in spokes that line up with the Shimano 105 logo in your photo. The spoke on the bottom is one position to the left of the one on top. That means it should go to the rim one hole to the left from the one on top. (directions based on the photo) If it doesn't that's the Hi-Lo.

If it is going to the right hole, the hub may be slightly rotated giving you alternating Hi-Lo spokes, but that would self resolve as you tighten the spokes.

Now, as to whether overly long spokes will still work, that depends on the amont of usable thread you have. Some spoke/nipple combination run out of thread and jam with the spoke about 1mm beyond the head, others allow much more overrun letting the spoke come up 4-5mm or so. Take any nipple and thread it on a spoke and see how much leeway you'll have. If it's very little, odds are you'll run out of thread, but if you have 2-3mm beyond the head you may skate by.

Only way to know for sure is to tighten a bit more (if the phasing is right) and see where it's headed. FYI, you usually need 2mm or so from where the spokes are tight enough to be straight.