http://www.slate.com/blogs/moneybox/2013/07/17/amtrak_s_unpe...
Although it is indeed inefficient and the MTA is completely inept, the platforms for LIRR trains are very narrow, they are shared by two trains and the escalators to get up to the main floor are also very narrow and crowded already.
So although the "mad dash" is in fact a mess, its a safer mess than overcrowding the platforms on the tracks.