According to the not-so-clear and ambiguous information from the Israeli immigrations website it is hard to obtain a definite answer.
On a personal note I have to say that if you are hired by Israelis you should ask them to deal with as much as possible of the process for you, even if it's just getting valid information, as the Israeli Immigrations Office is highly inefficient (from personal experience) and correct information is hard to come by.
Anyway, the official page on A2 from the Israeli Immigrations Office website states:
מי יכול להגיש בקשה
- נוכחות אישית חובה של הסטודנטים בנציגות ישראל במדינתם.
- השירות ניתן לסטודנטים ולתלמידי ישיבות שאינם תושבי ישראל.
- [stuff relevant for minors under 18]
Who can submit a request
- Physical presence is mandatory by the students in the Israeli consulate of their country.
- The service is given to students which are not Israeli citizens.
Further down the page it also states (original redacted - my translation):
How to submit a request
After filling the students' entry visa form you need to
personally arrive, with the proper documentation1, to the Immigrations
office closest to your home or to an Israeli consulate closest to your
I tried to keep the translation (specifically the bold parts) as closest to original as possible. It can be seen that it is not very clear whether your country and closest to your residence means your country of origin, or your current one. From the tone of the text, anyway, it feels like the emphasis is more on physical, personal appearance in a consulate, and less on which consulate it actually is.
 According to the same page, proper documentation means:
- An approval from the educational institute.
- An approval for paying tuition
- Proofs for means of subsistence (vague term, Google translated).
- Valid foreign passport (valid through the extent of the visa).
- Up-to-date passport pictures (to be attached to the request).
- Original birth certificate.