Whitetails sometimes happen because of defaulted buyers, but many times it's due to companies that want to maintain constant production rate, even though the qtr (or even year) didn't produce that...
Vertical CG is important in any maneuverable vehicle. Buses and trains have pretty docile mission profiles. A/C landing gear and handling characteristics would be hurt.
A lot of newer 'green' engines have less bleed air and accessory takeoff power available as compared to older engines...the think the article hinted about these issues being a problem area.
I agree with budget constraints and gold-plated USAF concerns, but if there was any time to replace these aircraft, now is the time! Don't waste time on the VLJs when you can get light biz jets...