I completely agree. Unfortunately there is a bug that prevents us from showing hints for 'separable' words (like "tussenin", in between). We really hope it will be fixed soon, but there is no telling how long the developers will take.
Another factor is that prepositions are largely idiomatic. There is not much that we can write in an explanation text, since there are no consistent rules. The only way to learn them is memorization through trial and error.
From my understanding, some verbs can have a preposition attached to the infinitive (aankomen, uitgaan, ...), and when the verb is conjugated the preposition separates and moves to the end of the sentence like that. In the infinitive it stays attached so you would say "Ik wil uitgaan" but "Ik ga uit"
You're right, both prepositions are a unit of meaning.
That being said, 'jongens' is not the subject of this sentence, but a part of the direct object.
Ik zit tussen de jongens in. >
Ik> subject: noun phrase: personal pronoun
zit > verb: finite verb: present tense
tussen de jongens in> direct object: prepositional phrase;
in.... tussen> head of the prepositional phrase (as it's a preposition)
de jongens> complement to the preposition: noun phrase. The label "complement" means that it's an obligatory part of the sentence.
I suppose the gaan...toe you mention is actually another case of a two part preposition: naartoe
But I too wonder why a normal tussen isn't good here. Maybe it's a subtle difference between position and direction? tussen would be me already being between them, tussenin would be me taking the seat that's between them?
My Dutch bf explained that when you say "ik zit tussen de jongens" (without the preposition "in") it can also have a slightly different meaning, for example, that you're one girl in a group of boys. When you say it with the preposition "ik zit tussen de jongens in" it means that you're sitting in between two boys.