Problem is, temperetures are significantly higher while my system is docked.
If I use my laptop without the station, the cpu and gpu temps are the same, or the gpu a few degrees lower. When it's docked, cpu temp rises by about 3-4 degrees (that would be still acceptable), and the gpu rises around 10-13 degrees, which is a huge difference.
There are two unrelated phenomena here:
1) Both CPU temps and GPU temps are a bit higher when docked. Most likely because some ventilation holes are blocked.
2) GPU temperature rises by several degrees when using DVI. This is a documented (although not fully understood) phenomenon
It's frustrating as it would be a perfect solution for using my laptop as a home computer with all my peripherials attached, but I don't want to shorten my laptop's life with these significantly higher working temperatures.
Don't worry about it. It will probably not shorten your laptop's life one bit. I've been running my T60 like this for years and in a somewhat warmer climate than yours, with the stock cooler and without any undervolting (right now its idling in the dock with CPU at 66C and GPU at 67C), and it is still going strong.
What about getting an advanced t60 dock with the pcie slot so you can put in an external gpu.
Unless you have specific needs, it's a waste of time, money and space. Nothing I have seen in this thread justifies it, IMO.