How to place minifigure legs into normal LDD bricks, like a 1x2 brick?
I see what you mean...  Friggin' annoying!  Can't do it Stud.io Ver 1.0 (157) either.  I haven't installed Stud.io 2.0 yet, to see if it's possible in the upgrade.  

Hmm...  You could... Just create a work-a-round that could potentially make your model a little more unique.   

These program issues are frustrating, but they're fun when they force us to think of an alternative.  

Here, try these Mech Fisticuff Gauntlets. The pictures look like nonsense, so let me explain the layout.

FRONT VIEW.
    

It reads loosely in columns from left to right.  Your new fist configuration build are the 4th and 5th Columns.


1st Column: Dark Gray 1x2 brick = Height 3 Plates.
2nd Column: Blue MiniFig Legs = Height 5 plates.
3rd Column: The total height of Legs and 1x2 brick.  = 8 plates high.
LDD won't let us stack a 1x2 brick on to leg stalk.
4th Column: Our alternate fist, fingers fully extended.  (Note: It
will be an unnoticeable 1/2 plate shorter then your original fists.
5th Column: Our alternate fist, fingers curled up, forming a Left
fist.
6th loose splatter pieces: Four individual pieces to our fist recipe.


93062 Skeleton Leg.
26047 Modified 1 x 1 Rounded with Handle.
99780 1 x 2 - 1 x 2 Inverted.
15573 Modified 1 x 2 with 1 Stud with Groove and Bottom Stud
  Holder (Jumper).

7th Pointing Hand of Prime.


Final Note: LEGO may not have those Skeleton legs in the colors we want in real life, but look through for other minifig leg or hinge+1x1 plate combination to get your Mech finger/knuckles right.    

EDIT=>HERE For reals. You can download my LDD file from my Google Drive, and import the alternate into your build file in LDD.  Save you some time.

BACK VIEW.


SICK VIEW.