Sophisticated Core 1.4.90, Sophisticated Storage 1.5.91, EMI 1.1.24 on Neoforge 1.21.1 version 21.1.248
When using EMI's Recipe Tree to craft a X quantity of items, it calculates the appropriate amounts to craft for each step. When using Sophisticated Storage's Crafting Upgrade's Crafting Table with EMI's keybinds to Craft to inventory, it overcrafts when using the "Craft All to Inventory" keybind. The "Craft One to Inventory" keybind works correctly.
Crafting with a Recipe tree:

After clicking the "Craft All to Inventory" keybind (overcrafts 48 instead of the 12 calculated by EMI).

If this is any help diagnosing why it does this, when using the "Craft All to Inventory" keybind, it will never craft more than 64 crafts at a time (not to confuse with 64 items).
This works correctly in the Crafting Station from tfarecnim, for example:

Sophisticated Core 1.4.90, Sophisticated Storage 1.5.91, EMI 1.1.24 on Neoforge 1.21.1 version 21.1.248
When using EMI's Recipe Tree to craft a X quantity of items, it calculates the appropriate amounts to craft for each step. When using Sophisticated Storage's Crafting Upgrade's Crafting Table with EMI's keybinds to Craft to inventory, it overcrafts when using the "Craft All to Inventory" keybind. The "Craft One to Inventory" keybind works correctly.
Crafting with a Recipe tree:

After clicking the "Craft All to Inventory" keybind (overcrafts 48 instead of the 12 calculated by EMI).

If this is any help diagnosing why it does this, when using the "Craft All to Inventory" keybind, it will never craft more than 64 crafts at a time (not to confuse with 64 items).
This works correctly in the Crafting Station from tfarecnim, for example: