There is a good discussion regarding this at:
http://www.concoursmustang.com/forum/index.php?topic=8441.0
Per that thread the red oxide primer was applied and then the floor pan was painted with a kind of black color (per the thread).
That thread referred to Dearborn production and the red oxide initial comment/question was addressed - and restated as much more likely batch paint.
I have a followup question regarding the under carriage. Where would the red-oxide remain exposed? Would it have been primarily in the drive shaft tunnel and wheel wells? In my case, I have a San Jose built in May of 65.
Rather than mixing different plants and time periods I suggest you ask the question above in a new thread. Given the projected build date of the OP's car it appears it is a Dearborn car
Would ask you to add the question to a prior thread about 65 San Jose undercarriages but could only find on that focuses on Feb 65 cars and they used different paint/primer sealer during that period than yours.
The 65 San Jose Undercarriage article in the Library section may answer some of your questions also
This is a undercarriage photo from my July 6 1964 mustang, also D-Code in Guardsman blue. This is how it looked before I bought the car. Hopfully it helps.
Looks like it may have been repainted or touched up. Unusual to see red oxide around your cars production period, on an early Dearborn car and though difficult to see the dolly mark locations don't appear to be bare metal. Seal sealer across the rear floor is suspect IMHO also shown in the picture
