Enumerating verbs where just one is used with preposition: correct placement?

This is a tool used for creating, collaborating on, and presenting design prototypes.

This is grammatically correct.

As you noted, this is the logical sequence of events: first create, then collaborate, finally present.

When you mix transitive verbs (i.e., which are immediately followed by their objects) and verbs that that take prepositions, I would suggest

• using the natural order, if there is any;
• if there is no natural order, ending with a transitive verb (thus avoiding ending with a preposition, and thus avoiding that the reader (initially) wrongly parses the sentence as if the proposition applies to all the verbs);
• and finally, if still possible, starting with a transitive verb (but this is just my æsthetic preference that can be ignored when other considerations take precedence).

Also, when the penultimate verb has a preposition, use a serial/Oxford/Harvard comma between the preposition and the conjunction, even if you normally don’t.

Your sentence checks all the boxes.