Thank you, Bloom. I will try TSRW when I have enough time. Maybe I can do everything tomorrow, depending on how difficult to use TSRW is.

Latest news:

I remade the jeans in TSRW and did what you told me about closing and reopening the work file when changing categories (in fact I did this after every step).
In TSRW it even does what we want (see attachment), but in game it looks even worse than my previous attempt (broken ankles in addition to the penguin arms). xD There must be something else I need to pay attention to.

By the way, my upload got approved in the state it was at the beginning of this thread. Link. I'm not planning to give up on the skin-tight boots thing, though. Your time has not been wasted, Bloom.

Did some testing and there is just one way to do this....clone the socks and load your pantstextures in that package.
This means it works as accesoire and you need a nude undiebottom mesh set as everyday(but i am sure it is already out there)
If you like i upload the mesh i used(undiebottomburnt).
This mesh has also a pregmorph.

I haven't tried it out yet but you might can set it as gloves so you still can use the basegame socks with the pants.(no idea wich texture will rule then)

Thank you, Bloom. I had already figured out that I could make my jeans as accessoires just like the countless leggings out there.
As a perfectionist, I'm just a little sad that there doesn't seem to be a 'proper' way of doing this, and it bugs me to see accessoires in my game that clearly are pants, not accessoires. Do not want. xD Other people might prefer this to having nothing, though. I will make an accessory version if someone asks for it.

I guess we can give up on the 'proper pants' now. Thanks for your help, I really appreciated that.

Personal i like these setups, gives you more possibility's, saves diskspace and loading time.

This is a bit of a necro, but I just spent an age googling to try and understand the texture layering, and this is one of the places it pointed me.
So I will reply here to pass along the info to any future cybernauts who may be trying to solve this issue.

I was playing about with a bodysuit and trying to work out why it would wrap over some shoes, but not others.
Seeing the guy earlier in the thread change a top into boots which would override bottom textures inspired me to track down the setting involved.
After scouring through text in CTU I noticed the "Unk 5" field for the Top and Outer shoes was 7, and for the inner boots 5.
Not editable in CTU though, so I had a trawl through cloned packages of the parts trying to find reference to that value.
Eventually found it in the CASP file with a name that makes sense "OverlayPriority".
Low numbers get layered on to the meshes before the higher ones, so higher number means more visible.
The basic convention seems to be this.

4: Socks and Gloves
5: Shoes\Boots that extend beyond the ankle.
6: Bottoms and Bodies
7: Tops and Shoes that are below the ankle.

So with the sims 3 package explorer I was able to change the priority for the jeans to achieve the required result.
What you do is open the package in s3pe, highlight CASP, then click Grid at the bottom.
Move down to where it says OverlayPriority 0x00000006, and change it to 0x00000005.
This is the same priority level as boots, and depending on what order you apply the clothes lets the boots be inside or outside the jeans. (see attached picture if it worked)

The fact this field was labeled properly in S3PE means this info was probably discovered long ago, but many of the tutorials for this game are either really old or completely missing.
I certainly couldn't find the exact setting to control the texture layering without digging around myself, so I hope it is of use to others.

http://www.modthesims.info/showthread.php?t=488263

Yeah I knew the info would be out there somewhere, trouble is tracking it down through the vast swathe of information on the internet.
Even using "sims 3 clothing layering" as a google search I am not finding your specific post.
Still newer replies and cross linking should help with visibility for all who don't know where the information is buried.