@ James
As far as I remember autohint.exe does not expect a pfa. You also can hint otf with it. And if you use the macro in FontLab, download the bugfixed version:
http://forum.fontlab.com/adobe-fdk-for-opentype-afdko/bug-in-autohintscript-belonging-to-the-afdko-25-21898-t7057.0.html;msg23917#msg23917.
(Makeotf expects pfa.)
Nevertheless this
I'll write such macro if I have some spare time...
would be cool.
The problem with the Fontlab macro is that it cannot create the flex hints that the command line version can.
Not the macro, but FontLab Studio. All you have to do is to activate flexhint generation in the FontInfo dialog of FLS (Not in the options dialog!). FLS will add the flexhinting. Note, that this will not destroy the autohinting from the macro! There is no disadvantage with regard to the macro. Just use the bug fixed version, because then you can choose, if you want to generate hints with or without replacement.
If you want to convince yourself, just autohint your font one time with the macro (with activated flexhint option) and one time from the command line (with flexhint option). Then decompile the name table of both font files with TTX and compare them with the help of a program like UltraCompare.