Northern Spain vs Southern Spain Sept/Oct

You have your N & S mixed up in the list of places. Anyway, the odds of better weather will be greater in the south - where it is too hot for many in the summer.

If you are using the trains, Renfe is the national operator but beware - their website does not show competing high speed train operators using the same tracks on certain routes.https://www.thetrainline.com does show the competing train operators and I would suggest you set the currency to Euros.

Where the weather will be better depends to some degree on your relative tolerance for heat (still a major potential issue in Seville/Cordoba at that time of year) vs. overcast/cool/rainy weather (possible at just about any time of year along the northern coast). You cannot count on beach weather along the northern coast on any particular day, even in July.

I'd suggest looking at the actual, historical, day-by-day weather statistics available on the website timeanddate.com to see the range of what you might experience in either area. Here's a link for Seville (with Cordoba, the hottest place on your list of options):

Seville weather -- September 2024

Use the pull-down box at the right, just above the graph, to change the month and year displayed. I like to check the most recent 5 years.

Use the Search box at the upper right to change the location.

Spain may be the most heterogeneous country in Europe, in terms of food, landscapes, climates, traditions, temperatures...and even looks. Northern Spain is wet, green, cool, mountainous (you can find mountains all over Spain, it´s the second most mountainous country in Europe), beautiful valleys and rough sea (this is the Atlantic). The South is also mountainous, but normally much drier and much warmer than the north. Two different worlds, Spain is a very diverse country. Just wondering what Terranova is (In Spanish, Terranova is Newfoundland!)

I have been all over Spain and love it all. My favorite cities are Toledo and Seville, but I loved the Basque region, Salamanca and Galacia as well.

One thing, I did visit Costa del Sol beaches and was a bit disappointing, they are not as nice at what you get in Florida or California.

I think that would be late enough for the heat in the south to have abated, and I don't know the rain stats for the north (like acraven, I make good use of weather websites for those details!). However, I don't think this is a weather conundrum but a question of which you wish to see more. They are so different to feel like completely different countries.
Since you would probably not be swimming but just enjoying the views and vibe of the seaside, I would be more drawn to the wild beaches of the north. The south is less impressive, though there are some nice stretches like east of Cadiz that I thought quite pretty. Both are seafood meccas (ekscrunchy can give you tons of ideas there).
I think you would want a car in the north if you intend to explore nature. In the south, the train system is so extensive that it is not necessary unless you really want to get out into the parks and such.
I'd keep digging though a comprehensive guide book like a Rough Guide to see what stands out. Things to figure out: do you want cities or small villages/countryside? (I am not seeing a lot of the latter in your proposed itineraries, though you said that was what you wanted). Second the transport issue--car for a portion or not at all?