The bigger issue is that the yard is easily the most convenient place to tie down an engine. Really the only other places are either on the Newington somewhere or at Rockingham, which is a hour from Portsmouth by train, so if the crew is running short on time...
Easiest solution would be to have Portsmouth pay Pan Am to put APUs in a handful of engines, include in whatever contract above that said engines need to be used on the Portsmouth Branch, and APUs need to be maintained in working condition, except when off for repairs or inspection, and go from there.