Yes, the camera is stop-down metering only with the TTL Pentaprism Finder and extension tube. And switching the lens back to AUTO after metering only gives you a brighter viewing area and easier focus; otherwise, it is an optional step. It is normal for the metering needle to rise to the '+' when the camera body is not coupled to an automatic diaphragm lens.
When you attach an extension tube to the camera body, the only interface between the extension tube and the camera body is the aperture lever. When You push the shutter button, the camera body lever moves the lever in the extension tube which thereby moves the aperture lever on the lens. So it doesn't make any sense that the exposure would be different with the lens set in MAN or AUTO with an extension tube unless something is not working correctly like changing the aperture.
You can verify this by inspection:
- Mount an extension tube and lens.
- Configure the camera to fire without any film.
- Put the camera in bulb mode.
- Set the lens to, say, f8.
- Set the lens to MAN mode.
- Press and hold the shutter button.
- Look at the aperture blades diameter through the lens front element.
- While still holding the shutter button down, switch the lens to AUTO mode.
The aperture diameter should not change and therefore neither should the exposure (also check the reverse of AUTO/MAN in the procedure).
Also be aware if you are using an external meter, you need to correct the exposure by adding additional exposure which is dependent on the length of the extension tube. For example, you need to add approximately a 1/2-stop of more exposure in the case of the #1 ext tube and 105mm lens. The extension tube manual has a table of exposure correction factors when metering without the TTL Pentaprism.