Yes, Megaventory can handle that with the Works module.
Let's say for example that you buy individual products with SKU: SKU001 and you combine 24 such products and sell them in cases of 24.
You should enable the Works module in Megavetory (Admin > Setup > Enable Works) and then create those 24x1 SKU001 (1 box:SKU001-case) also as a bundle product in Magento (SKU001-case = 24xSKU001). The individual SKU001 products should also remain as simple products in Magento.
The Magento order will go through in Megaventory as SKU001-case and Megaventory will also create a Work Order to "create" this box from the 24 items. The Work Order is also responsible of "consuming" the simple items to finally receive the box. Please also receive in the user manual or our knowledge base for more info on the Work Order. This setting will also allow you to keep stock of the SKU001-case item, something that Magento cannot support on its own without the Megaventory extension.