SoCal,
I believe that it is very clear that miles earned from the transfering of Amex or Diner's points do not qualify for elite status on TWA (though other partner mileage does count). When the November transfer date comes around AA also said that they will add in all of your TWA earned flown miles with the AA flown miles to determine elite status.
If I were you I would put all my TWA miles on my AA account so that (as you said) I would get the 100% bonus miles and credit towards the 500-mile upgrade certs. I do not see any downside here - other than the difficulty some elite TWA members have had when trying to upgrade their TWA flights, but there are ways around that.
ff