Something has bugged me, if you look in the...Fallout4 - Meshes.ba2...so is the toilet a non broken one for tha player house (the one you can build in workshop), but in game it is a broken toilet with the cover and seat on the side and all...any fix for this?

Use a bucket...

I did, it added to the ambience of the shackmansion.

Never mind i have fixed it.

Just curious, you picked-up and set down or scrapped and put a new one in?

Most of the toilets in houses can only be scrapped, bad part is that the vanilla toilet you can replace it with in the workshop is as bad or worse. Thank god for mods!