So loser of Game 3 would come back faster to play Loser of Game 1 in Game 5, the first game of the 2nd day. Loser of Game 4 would need to come back "faster" to play loser of Game 2 in the second game of Day 2, Game 6.
What happens with weather postponements when Game 4 starts at 10 AM on Day 2 and Game 6 starts at 6 PM later that day? Loser of Game 2 would be much more rested.
No... This doesn't come into play until the end of the second round, so the first 8 games remain set up exactly as they are now.
Using this year's bracket as a reference piece, once Marietta lost to Salisbury and La Grange lost to ECSU, they would've swapped pools. La Grange would've faced UWSP in an elimination game while Marietta would've played Trinity.
I can see your point though in this situation as La Grange played the last game of Day #2 and then would be scheduled for the first game of Day #3. That said, you could flip flop the La Grange vs UWSP and Marietta vs Salisbury games to give La Grange the second game of Day #3, which is when they played this year anyway.