You missed an important detail:
Given sufficient capacity (see below), a construction element can fortify any other element from its maximum self-fortification level to the maximum fortification level in 90 days.
emphasis mine. Point being, the 90-day rule applies to elements,
not formations, so all is WAI.
This means that the intention is not to be able to fortify an entire formation to maximum, but one element at a time. An element, if you don't know the definition in this case, is the set of units in a formation which share a class - so if I have a formation of 1,000 INF+PW and 250 INF+LB, there are two elements: the first element is 1,000 INF+PW, and the second element is 250 INF+LB, both of which are 5,000 tons in size.
The way your CON will interact with this formation is that it will dedicate 5,000 tons of its fortification capacity to each element, with 2,168 tons left over which will be dedicated to some other element(s) in some other formation. If the formation has a third element of 250 INF+LAV, that element will receive the remaining 2,168 tons but since it is 4,000 tons in size will only fortify at a bit over half the maximum rate.
This does mean in general that large amount of CON are mostly useful for fortifying permanent units. They can be useful for emplacing relatively hasty defenses (in, say, 90 or 180 days in anticipation of an enemy attack), because even fortifying a portion of your force can still make your defense more stubborn, but you won't be fortifying a massive army in 90 days unless it is mostly CON.
Also note that there is a sort based on maximum fortification, so you will see your STOs, INF, and other STA elements fortified first. If you don't care about your armored vehicles fortifying (perhaps you prefer them on Front Line Attack stance) then the time to achieve a practical fortification level for a mixed army is less as well.