The SCW was basically a conflict between progressive intellectuals who wanted to improve the nation getting rid of the backwards militarism and dreams of grandeur, and conservative military-men who wanted to improve the nation getting rid of selfish politicians who didn't serve Spain but their own interests. It's an extreme simplification but that's roughly the base. Both sides claimed to be the solution to the "Problem of Spain" and both developed as different interpretations of the defeat in the 1898 War and its consequences. Butterflying one war would have butterflied the other. Period. I'm sure neither Sagasta nor Roosevelt, McKinley or Montojo could ever have imagined what the decisions they made those days were going to cause 40 years later.
Still, if there is a freaking civil war in the 1930s the size it was in OTL (as almost every ATL taking place in the 20th century seems to want to) that would mean Cuba (if it is still Spanish, which is a long shot itself) and Puerto Rico would have been largely autonomous and independent-minded during 30 years, so they would simply break out with little resistance. The Philippines would most likely still be a colony but under a strong military presence after repeated uprisings, and said military presence would most likely be commanded by very hard line conservative officers (Millán Astray and the like comes to mind). Not just to keep the Filipinos in line, but also to have those military-men far from Spain itself, a common practice in the 19th and 20th centuries (in fact, Franco was destined to the Canaries in 1936 for similar reasons, but it seems they were too close to the Peninsula to avoid a providential trip on plane). It seems likely that the Philippines would experience another revolt then, a perfect excuse for Japan* to jump in with the supposing intention of "bringing order". Looking how they treated the Spanish community in Manila in OTL, it seems that the Japanese penetration and subsequent presence would be anything but pleasant.
But as I say the polarization in the country isn't really what I would expect. In my opinion, the country would just evolve towards a true parliamentary system as it was doing till Primo de Rivera's coup in 1923, yet in an ATL this event would have been butterflied.
A wild card, however, is if Spain joins WWI in the ATL. In OTL it wasn't likely after the Spanish-American War, but in TTL Spain still has an overseas empire that needs British and French friendly relations to survive, and it is ambitioned by Germany. Remember the Germans actually tried to seize the Spanish Polinesia in the 1880s and achieved to receive economic concessions there in order to get out. Without losing the Philippines, Spain would have not sold her Polinesia to Germany in 1899, but Germany would have insisted and caused a worsening of relations between the two countries in the turn-of-the-century. Then, add the unrestricted submarine warfare of 1914, which sank many Spanish fishing ships in OTL**, and you have enough reasons to see Spain jumping in the conflict on the Entente side like Portugal and the USA did. The war would have been a serious hit to the economy, even if there aren't true fronts (as was the case of Portugal and Japan) and the peace would have been perceived as “mutilated”. End of German concessions in the Marianas and probably a slight modification of the frontiers in Morocco and Guinea seem probable changes at Versailles and successors, but that would be seen as insufficient by the populace. That, combined with the effects of the 1929 Crash, would lead to the rising of fascist parties in the country and possibly to a fascist takeover in the early 30s... a peaceful one, like the ones of Italy and Portugal. You can even end with a Spain that has not gone through the destruction of the civil war becoming a full member of the Axis, and with a navy of at least the size of the Italian. With Japan possibly ignoring SE Asia and no sanctions nor Pearl Harbour, there is a chance of your average "No US in WW2 leads to an Axis Victory" TL taking place.
-------------------------------------------------------------------------
*It's not likely Japan would try to grab the Philipines earlier than WWI. Not just because Japan was weaker and more preoccupied with Russia, but also because that would mean a pagan yellow nation taking over millions of Catholics, and that was too much to be tolerated by the great powers back in the old days. After a destructive world war and with a rising Nazi Germany in Europe, the situation is obviously very different.
**The respond of Spain in OTL was closing the Spanish ports to German ships and handing all the German U-Boats captured to the allies. Apart, of course, of diplomatic protests.