You can upgrade a transporter/colonizer to a ship with a lower population capacity (less modules) without diminishing the boarded population.

It should either disallow this when the number of boarded population exceeds the maximum capacity of the ship you wish to upgrade to; or the boarded population should be diminished to the max population of the new ship.

Currently the following 'cheat' is possible: Build a transporter with nothing but transport modules; load maximum population ; Upgrade the transporter to one with only one transporter module and a maximum of engine power; outrun enemy fleets and take even their strongest planets.*

* this assumes that the planet has no ships in orbit.

The current situation:

"Good afternoon,
This is your captain speaking.
We  are going to upgrade our ship; for the remainder of the journey you have to double bunk and split share your oxygen.
Have a pleasant continuation of the journey."

The passengers happily agree to the new level of travel comfort.

What it should be, either:

"Good afternoon,
This is your captain speaking.
We  are going to upgrade our ship; for the remainder of the journey you have to double bunk and split share your oxygen.
Have a pleasant continuation of the journey."

The passengers rebel and the upgrade is not performed. Also, the captain's head mysteriously went missing, but that had nothing to do with the proposed ship upgrade.

or:

"Good afternoon,
This is your captain speaking.
We are going to upgrade our ship; will the following 5 billion people report to the airlock for the upgrade party."

The passengers drink the offered beverages and in ecstasy of the drug induced haze jump into the vacuum of space.

The upgrade to the "Fast Long Range Transporter"

After the upgrade the "Fast Long Range Transporter" hold a population of 10.

However the "Fast Long Range Transporter" has only 1 "Transport Module" with capacity of 5.