When you look at the numbers in Hotel Savings by Building and Hotel Savings by Departments reports, you will notice that it only includes employees and rooms assigned to department.
Also, some em.emid do not match the rmptc.emid but they are counted.

From the help file:
• total bar = SELECT count(distinct rmpct.emid) FROM rmpct, em WHERE {rmpct values meet filter restriction} AND rmpct.emid = em.emid AND WHERE rmpct.visitorid IS NULL GROUP BY rmpct.dp_id

• available bar = SELECT sum(rm.capem - rm.countem) FROM rm WHERE {rm values meet filter restriction other than Dates} AND rm.hotelable = 1 GROUP BY rm.dp_id

We would like for rooms that don't have a department assigned to also be counted in the report and for the employee in rmpct table that do not match employee in em table to not be counted?