I think that in the first (ambiguous) phrasing there is an implicit (common-sense?) understanding of: the employee shall be reimbursed for all expenses if the employee asks for it or wants it, ie the employee has the right to ask for and only then the employer has the obligation to reimburse all expenses.
No, there is no reason to appeal to "common sense." It is the plain and unambiguous meaning of the text itself.
I think you may have been reading too many IETF documents.
Legal text doesn't come with a list of definitions that attempt to lock e.g. "shall" down in stone.
I rarely read IETF documents. But as a practicing lawyer for about 15 years, I've read, interpreted, drafted, advised on, and litigated countless uses of the word "shall" in agreements (as well as in statutes and regulations). In fact my first pro bono case in BigLaw, on behalf of a nonprofit in a corporate election case, hinged on it. Shall is not this mysterious ambiguous beast the link makes it out to be.
It also violates the fundamental rule that changing a sentence into the passive voice does not effect a semantic change.
"The employee shall be reimbursed [by the employer] for all expenses." must necessarily mean the same as "The employer shall reimburse the employee for all expenses."