A few facts here. I own a '93 Escort wagon. Bought it from BobFL. Haven't towed it yet, but plan to. I also happen to own a Festiva, that I have towed, and take care of a couple Aspires.
A little on the Festiva/Aspire Escort lineage. They both share Mazda roots. Festiva/Aspire was simply rebadged Mazdas, Escort was based on a Mazda platform. What matters here is that the manual transmissions, while completely different, were both Mazda transmissions essentially. Both are traditional type manual transmissions. Festiva had a four speed for it's first two years, and a five speed was optional in the second year and then standard after that. All Aspires and Escorts were five speeds. The 4 speed Festiva transmission had a spacer in place of the fifth gearset, the rest of the transmission was the same.
I can think of no reason either car, when equipped with a manual transmission, couldn't be flat towed in neutral. There's nothing in the transmission that needs the engine to be run. No fluid pump, no electrical components.
I'll dig a little around here (I work in Dearborn) and see if I can come up with why Ford wouldn't recommend towing. Probbaly as simple as they never tested it, so they won't recommend it.