The actual transmission loss is definitely in the 15% to 20% range for most transmissions, that is, engine to rear hubs, but it is not that simple.
The losses arise from two main causes, sliding friction in the helical cut gears producing oil shear, and oil churning/windage losses. Forget about ball bearings and uni joints, their losses are insignificant.
Oil churning losses are going to be highest at high Rpm and very low loads. Oil shear from the continuous transmission of very high torque heats the oil signifying a definite frictional power loss. Anyhow, the average at full power is in the range of 15% to 20% for most transmissions.
The biggest problem with roller dynamometers are the tyres. Even if there is not much slip, power transmission by friction into a relatively small diameter roller through a small arc of contact is not going to be very efficient. So very much can depend on tyre pressure, wheel diameter, and how hard you tie down the car. Losses of 25% to 30% are sometimes claimed between flyweel power and measured rear wheel power. Hub dynos have none of these tyre related problems, and always read consistently higher than roller dynamometers.
Transmissin losses also vary with engine Rpm and gear ratio, and how the extra power is obtained. Suppose you modify two identical production engines. One is n/a and spins to silly Rpm and develops 400 Hp. The other runs a supercharger at enormous boost pressure and also develops 400 Hp, but at half the Rpm.
Put through identical transmissions and both run in the same gear, the rear wheel Hp on a roller dynamometer will quite likely be very different, even though the flywheel power of both is identical. The n/a car will have twice the roller speed at half the torque. Try changing tyre pressures, or tie down both cars differently, and everything changes.
That is probably why Fred's dyno reads differentkly to Joe's dyno, the rollers are different diameters, and Fred has a different system of holding the car down on the rollers. Joes rollers have a non slip surface. Both dynos are perfectly accurate, but read differently. So whose dyno is right, Fred's or Joe's ?
Don't worry about it. If it reads more after you have modified it, be happy.