Well, support told me it couldn't be done. I got no love on the forum either.
We figured it out ourselves.
If this will help anyone, for $10 I will tell you how we did it.
Oh, what the hell, I will tell you for free.
Short version:
Create a group that controls what price you want a set of users to have and also create a separate group that controls what that same set of users can see within the store. Assign that set of users to both of those groups.
In more detail:
I create a group called "50_Percent_Markup" and one called "60_Percent_Markup". Set up Dynamic Pricing with the correct prices and tie it to these groups. Allow these pricing groups to only see products that are shared across multiple user groups.
Create user groups to control what rights the users have within the store as you normally would. In this example: Company1Employees, Company1Managers, Company2Employees, Company2Managers
Now assign users to the two correct groups:
Company1Employees, 50_Percent_Markup
Company1Managers, 50_Percent_Markup
Company2Employees, 60_Percent_Markup
Company2Managers, 60_Percent_Markup
Now everyone in company 1 gets a 50 percent markup price, but still only has rights as laid out by whichever Employees/Managers group they belong to. Company 2 is the same but with the 60 percent markup prices.
This was probably a waste of time, but there you go.