The user with the permission that blocks them from viewing certain types of data will not be able to see the custom columns. If a user cannot access a report column, they will not be able to view any custom columns derived from that column. For example, if you create, in a public report, a custom column called Gross Margin that includes the Cost Amount (BC) field, but a user cannot access that column because they do not have Show project cost data permission, they will not be able to see the Gross Margin custom column either.