MacGyver travels to 2 countries in the 7th. season- in "Honest Abe" and "The Mountain of Youth". But you're right- only "The Mountain of Youth" is fully set in another country.
Also, I think kinda the beauty of the Phoenix Foundation job is that it was somewhat part-time, but probably due to the nature of work MacGyver was doing, it paid enough to take care of his bills. And they of course, also did special things for him from time to time- like setting up a scrimmage with a professional ice hockey team or getting a scholarship for Lisa (from "Nightmares") (both of these he mentions in "D.O.A. MacGyver")........(Why yes, I DID just recently watch that episode.

)
So while MacGyver does plenty of assignments for Phoenix, he also has the leeway to do stuff on his own. I suppose we don't necessarily know when all of the episodes are set- so perhaps some of the "social conscience" episodes are set on the weekends when he has free time to work with other causes and concerns- like the stuff he does with the Challengers Club.
But to be fair- from the 4th. season onward, MacGyver still does plenty of assignments for the Phoenix Foundation.
"On a Wing and a Prayer", "Collision Course", "The Survivors", "Deadly Dreams" (I'm pretty sure working with Lt. Murphy and the police department was sanctioned by Phoenix and not just something he was doing for fun

)
And there's cases like "Ma Dalton" (which I think you can make an exception for. Every now and then, MacGyver runs into things like this on his own that Pete goes along with and lets him work on- so I think you could still consider it a Phoenix mission, of sorts in any case.)
And if you go with that understanding, that would apply to a lot of other episodes, including "Cleo Rocks", "Fraternity of Thieves" (and that was a personal thing for Pete!) "Runners" (though he was working with Pete on Phoenix work when he ran into Jenny), "Gold Rush", "The Invisible Killer", "Brainwashed", "Renegade".
For the 5th. season-
"The Black Corsage", "Cease Fire", "Second Chance", "Children of Light", "Black Rhino", "The Ten Percent Solution", "Two Times Trouble"
and
"Serenity" (where MacGyver specifically refuses an assignment because he's been getting too many without enough rest! And because Pete just assumed he'd do it without really asking him first) (but don't worry- they patch things up at the end!

)
"Live and Learn" (probably would be considered a "social conscience" episode- and it was a Phoenix-sanctioned project)
"Jenny's Chance" (another something that MacGyver runs into that he pulls Pete into- I'm sure Phoenix isn't upset that MacGyver's bringing in a notorious money-launderer, so I feel like they would count something like this towards his work for the organization)
"Deep Cover", "Passages"
Season 6-
"Humanity", "The Gun" (obviously Pete does work with The Challengers Club from time to time as well- as we also saw in "The Madonna"), "The Wall", "Lesson in Evil",
"Bitter Harvest" (I tend to feel that these kind of adventures MacGyver runs into would or should give him credit with Phoenix for doing work- especially when he calls Pete in to do legwork for him.)
"Jerico Games", "The Wasteland", "High Control" (the scene at the start definitely counts in any case), "Blind Faith", "Faith, Hope & Charity" (tracking the gray wolf for Phoenix), "Trail of Tears"
Season 7-
"Obsessed", "The Prometheus Syndrome" (I'd count it towards credit with Phoenix), "The Stringer" and "The Mountain of Youth"
And it's understandable as to why MacGyver didn't have many direct Phoenix Foundation assignments in the 7th. season, as Dana Elcar was not showing up too much as Pete, probably due to his dealing with glaucoma. But at least he was kept on the show and still did some of his best episodes- obviously "Obsessed" and "Good Knight, MacGyver" (Parts 1 and 2)- and "The Stringer", of course.
I think it's cool that MacGyver had a job flexible enough to let him do side projects on his own and obviously that paid him well enough to take care of his financial needs and everything. Just because he didn't have a general showing up while he's sunbathing on the beach and sending him off to Burma to retrieve a downed weapon all the time (like in Season One's "The Golden Triangle"- and even there he did a "side project"- I'd call freeing people from slavery a "social conscience" episode) - that doesn't mean he wasn't still doing work with Phoenix and still accomplishing a lot of good, even if it was just a "smaller" thing for a friend.
Man, (except for the really dangerous stuff and good possibility of getting killed

) I'd love a job like that!