When lini use his hability to discard one card to get one 10dice in Dexterity and you use a Mastertool that gives you 2 aditional dice to disable a barrier, only gives you 2D4 , i believe its wrong.

 

In the adventure - story mode - here comes the flood , the creature get points when discard an ally but  the true its that he gets points for discard any card, For this its imposible to win.

Regarding your first question, Thieves Tools and Masterwork Tools only add dice to your Disable Check, which is a skill that Lini does not have.  Even if she activates Beast Mode and gets to roll a d10 for Dexterity,when you roll a check that your character doesn't have, you use a d4.

 

And for your second question, in Here Comes the Flood the counter for the Villain doesn't show how many allies he's captured, but how many cards he's taken.  Only at the end of the scenario do you compare the number of allies captured.  You aren't supposed to find out until the end.

Yeah, most of characters carry xTools, but - other than Merisiel - they are there for the discard/recharge usage. Nevertheless, it's really useful to not have to spend a Blessing on passing a Barrier check.