We also encountered this issue some time ago and this is what M2e answered on an email:
Thank you for provided details.
I checked your FBA order XXXX and I understand that you
want Magento order creation for FBA orders do not depend on stock
availability.
Let me please explain the logic how Magento orders are created. When
a channel order is imported in M2e Pro, M2e Pro checks settings
provided in Account settings > Orders tab. If corresponding settings
for Magento order creation are provided - M2E Pro sends a request to
Magento to create a Magento order for the channel order.
Magento orders are created due to Standard Magento functionality and
Core Models. Magento does not let to create an order if the product is
out of stock or 'disabled' or does not have available qty in Magento.
These requirements should be met so that the order was successfully
created.
M2e Pro cannot affect the logic of Magento orders creation process.
You can temporarily set 'in stock' status and qty available if you
want Magento order to be created at one for FBA order.
Hope this explanation will be helpful. Please let me know if I can
assist you with something else.
Next email:
Other our customers use backorders feature. As a possible workaround
for creation orders when product quantity is 0, you can allow for
needed products (product should be in stock, manage quantity - "yes".
This will allow Magento order creation for corresponding FBA order if
qty=0. You can set this parameter in Magento product inventory.
I have consulted with our development department on your case. As a
possible workaround, we can provide you with a part of the code which
is responsible for orders functionality. If your developers would be
able to adjust the needed changes, we would be glad to assist you.
Please also note, that we will not guarantee the proper work when some
custom modifications to the code are applied. In case this suggestion
is approved by your developers, please send us your confirmation and I
will send you a part of the code.
The code they wanted to provide was useless, it was just a hint that the magic happens in
app/code/community/Ess/M2ePro/Model/Order.php
public function createMagentoOrder()
which is quite obvious.
Please consider that backorders feature will bring other issues, so we do not use this and currently live with this situation as it is.
For me it is a quite important and standard situation to have FBA stock but no magento stock, so I don't understand why they don't fix the problem.
When time is available we will do a fix ourselves.