Slightly OT, but I have found these differences exist when booking paid flights, as well. Not just differences in availability (sometimes more seats available on the long haul when originating at a Spanish provincial airport and routing through MAD), and lower prices, as well.
Santander has seemed particularly good in the past. BCN will give you some sort of discount on transatlantic flights through MAD. Other cities are hit-and-miss.
Early in 2016 I did dummy bookings, Business Class, from various Spanish and European cities to SCL on Iberia, and return.
At that time it was 800 Euros cheaper to originate in Dublin than in MAD, and originating in BIO was more than 1000 Euros cheaper than orginating in MAD.
YMMV, but always worth having a look.
Buen viaje!