One flaw might be that the robot will tip easier. If that is not a problem then I think having a shorter drivetrain would be better. You would be able to turn around in tighter areas. I don’t think that cutting it would lead to an easier lineup, but I couldn’t say for certain. If I could see a picture of your robot, it would really help.
Yes cutting down the drive train would help, but as tutman96 said you might run into more tipping issues. While your wheels might still be at the same locations relative to each other, cutting the drive train will take off the front pieces of metal which were probably acting as anti-tip mechanisms in and off themselves.
My team has a vertical intake with a 15" long, and 17.75" wide chassis with a 6 omni-wheel drive. I don’t know your exact bot design, but our chassis performs very well. It is not tippy, and it is pretty easy for our scoring.
I think that the whole lining up issue will always be a problem with a vertical intake unless you can get your intake all the way over the 30" goal, and some how “lock” it into place. But having a shorter chassis gives you the option of extending and/or placing your intake past the front of the chassis to allow easier scoring.