I've been rewatching the show again lately.

And I've actually noticed that when the Doctor is in front of the console, he almost ocuppies a whole side of it, however, in the game, just one side is almos as high as the character, and too wide.

I've tried other Doctor Who mods like DWCM or Tardis Mod, and prefer this one in many aspects but i think that the consoles are too big, I've seen some update 46 beta reviews and they are pretty well made, perfect size, it's just a personal preference issue, but maybe someone else has noticed this, and I felt the need of saying this.

Yes the sizes are different, but that's because real life scale is very different to Minecraft scale.

The block-built consoles need to be as wide as they are to fit certain controls on them.
Also you're dealing with the issue of Minecraft block angles. For example let's take the Toyota console in the mod right now. The scale for each panel is just right as each panel is represented by a model placed on a stair block. The only issue is we can't place stairs at an angle, like the TV show console, so it looks like it's bigger. 

And for the consoles you saw in the Update 46 Test build videos, they are modeled consoles. Some of these are already in the mod and there will be some new ones in the next update. Players have the choice on which they want to use. The console rooms are usually built with block-built consoles rather than modeled as may people prefer block-built as it fits the Minecraft style more.

 Then I don't mind if you can choose whatever you want.

I think the update 46 is going to be cool xD