Bushmaster is also set in Central America as well as Jack of Lies (than you can say Vasquez has a twin). But to be honest, I think we're dealing with different countries each time since Mac and Kate Connolly met each other in San Sebastian and Mac and Jack flew to Barraca to safe Pete and sister Clara. I don't think it was the purpose of the creators to take Mac back to the same location each time he was going to Central America.
If it all was one country you can say Mac, Pete and Jack were involved in one big plot to overthrow a corrupt government and help Samantha Lora to win an election. But I think there is a lot more to it than just taking out General Vasquez or Rafael. Generals are mostly puppets to a dictator. Look at Murdoc and Delasora. Delasora didn't need him anymore in the end.
To take down a dictatorship wars are fought out sometimes on world scale (WWII) or smalltime civil wars in distant countries or even the war on terror.
I think that the 1980's were Noriega times since he was mentioned in On A Wing And A Prayer. I think that issues like that fitted in the MacGyver Universe so it's possible that made it a recurring theme. If MacGyver was made now he'd be all over the Middle East (Iraq, Iran, Afghanistan, Pakistan, Palestina, Israel) or North Africa with the Arabian Spring.
So to be honest I think you're overthinking too much but for the sake of fanfic in might work.
Say that Delasora is the dictator of a fictious country in Central America and every little town that was visited by Mac throughout the show is a part of that country. Every general in those episodes have their own armies to keep the towns down. So Vasquez (helped by Ryerson), his evil twin brother Antunnez (helped by Sonny), Salazar, Rafael (than still helped by Santina) are part of the Supreme Command terrorizing their citizens. Than we have Colonel Cardosa and Ramos under the generals trying to kill Samantha Lora who at that time is being helped by Mac and Pete. She wins the election gets around the table with peoples that you can reason with along with the United Nations and the Phoenix Foundation on neutral soil let say um... Switzerland. Where the remaining rebels plots to take out Samantha Lora but Mac stops them and gets shot instead... oh, wait that's Cease Fire.
There might be a good storyline here. I really have to get back into writing. But I really think this one requiers some work if you want to do it decently.
I think the poison that was used was applied to this knife, passed to the mutton when it was cut and then activated by the wine. - MacGyver.
Sometimes you just have to die a little inside to be reborn and rise again as a stronger and wiser version of you.
It's better to be a little sad than to be fake content.