How to set a rule that sets a term reference field value and text area value in a commerce order entity
Here's a strategy that I think will work:


Create a field on the product like field_bulk_order_limit
Create a field on the order called "field_held_bulk_order" or something. This can be a boolean or some similar thing.
Create a rule that looks at the product's field_bulk_order limit whenever a line item is created or updated and its product has that field. It could output to the screen (system: site message) at the user if the number is above the bulk order limit.
Create a checkout rule (a rule triggered by "when completing the checkout process") that loops through the line items and checks their products' field_bulk_order_limit. If it finds line items with a quantity higher than the field_bulk_order_limit, set the order's field_held_bulk_order to TRUE. Optionally also show them another message.
Fiddle with your administrative order views to have a view that explicitly shows held orders,etc.
Nice to have: create a custom pane that lets them enter the reason that they need so many. This requires a tiny module. It could imitate the commerce_order.module's pane (see commerce_order.checkout_pane.inc and commerce_order_commerce_checkout_pane_info()