According to the BSA Guide to Advancement, alternate merit badges CAN count toward the four Eagle required badges needed for Star rank, or the additional three Eagle required MBs needed for Life rank. I have boys with both Swimming and Cycling and initially had TroopTrack only counting Swimming toward their Star rank and Cycling toward Eagle palms. But, using multiple “alternates” is perfectly legal. TroopTrack users have control over whether to apply an alternate merit badge to Star or Life rank or to Eagle Palms via the “Applies to Rank” dropdown in the edit popup.
"188.8.131.52 Earning Eagle-Required Merit Badges for Star or Life Rank
Candidates for Star or Life, in the selection of “any four” or “any three,” respectively, of the merit badges required for Eagle, may choose from all those listed, including where alternatives are available: Emergency Preparedness OR Lifesaving; Cycling OR Hiking OR Swimming; and Environmental Science OR Sustainability. For example, if a Scout earns Cycling, Hiking, and Swimming, all three of them count as Eagle-required for Life rank. Only one, however, would serve toward the required merit badges for the Eagle Scout rank. The other two would count toward the optional merit badges required to make up the total of 21 merit badges.
Note that Star and Life requirements each allow two non-Eagle-required merit badges. It is the Scout’s decision, however, to earn more—or all—of his Star and Life badges from the Eagle-required list. "
Italics above are mine, added for emphasis.