For example, a small probe can be made on the ship within 10 minutes, but a colony on the planet is built for many months or years (of real time).
A space game on the scale of entire galaxies that doesn't have timewarp sounds rather boring. I mean, I won't be buying a game based upon SpaceEngine if it takes literal years just to build some colonies to upgrade.
In all honesty, taking months of real time to fully establish a interstellar colony doesn't sound all that unreasonable. Bear in mind that this is a space-
simulator, not just a space-game like Dangerous: Elite. Besides, you will have plenty of other things to do in the mean time, such as establishing other colonies, building interplanetary infrastructure, making interstellar trade routes, exploring stuff, researching tech-trees, etc. As long as the wait times are balanced with other activities like those aforementioned and even some optional stuff like combat, it should be a good experience. I would also expect terra-forming to take a long tome as well, since physically changing a planets surface is a arduous and immense task.