Hello @Work24X7 welcome, you generally need to find apps from the same developer to expect things like this to interoperate. Example Boldcommerce options app and discounts apps.
If options do not affect prices or skus get rid of the variant options app and bake it into the theme as a customization. https://community.shopify.com/topic/616503
There are also automation apps like usemechanic that could be scripted to create draft orders with specific pricing or generate custom discounts.
https://tasks.mechanic.dev/create-a-draft-order-from-the-cart
https://tasks.mechanic.dev/generate-a-discount-code-when-a-certain-product-is-purchased
The only solution I can come up with is creating a second wholesale-only store, but that’s a pricey solution
If the wholesale offering isn’t profitable why are you doing it?
It’s much saner to sync inventory on the backend of two different shopify stores than it is to get various random frontend apps to work in tandem with other random backend apps.
Not to mention user mgmt, content mgmt, marketing, discounts, design, etc etc.
You can also always try to negotiate a lower rate for having multiple stores.
If a store is on the enterprise Plus plan either use checkout-scripts, the dedicated wholesale channel or an expansion store covered by that plan.