The former Barcelona teammates both started last Wednesday's 4-0 win over Toronto FC, but then left late in the first half and didn't travel with the team for Sunday's 1-1 draw against Orlando City SC.
The leg injury to Messi, who also missed Miami's loss in Atlanta 10 days ago, has been described as an old scar tissue problem, while Alba continues to deal with muscle soreness.
When asked Tuesday about how the decisions regarding Messi's availability are made, Martino said it's a true team effort.
"In this case, we sit with him asking how he feels," Martino said. "Maybe other players, one makes a decision, but here we will make a decision we are in agreement over.
"Here, there are questions. The player, the [U.S. Open Cup] final, and what comes after. These three scenarios have to be evaluated; it is not just about the next game. Risk is always there, but we try to decrease the margin of risk."
That risk level, Martino admitted, is going to be assessed a little differently because of what is riding on Wednesday's result.
"If it wasn't a final, we wouldn't take any risk, but because it is a final, there is a chance we take that risk," Martino added.
Martino also shrugged off any suggestion about the team being purposefully over-secretive regarding Messi's injury situation.
"We are not trying to be mysterious with Leo. I say this with knowledge because of my time with Atlanta," Martino said. "Weekly there are reports of injuries and which players travel and don't travel. This is a special situation. And if Leo were not here, we would not be discussing this.
"This is part of football. We are talking about the best player in football, and I have to give an answer that could affect the structure of the rival team. Why should I give that information if I can keep it to myself?
"We understand the desire [for the fans] to know, but we are not trying to be mysterious. We have a real situation."
Things won't get any easier for Martino and his Messi situation, as, starting with Saturday's home contest against New York City FC, Miami will face yet another period of severe congestion, with three games in eight days, as it continues to push for a spot in the MLS Cup playoffs.