It is not a percentage. I thought so too.
Try this: Start with a new Thor, and initialize the patch. Choose any filter for the first filter slot (I would recommend the "Low Pass Ladder Filter" for this test, and set the slope to 24 Type I.) Set the frequency AND the "Env" knob on the Low Pass Ladder Filter to zero. There should be no sound at all when you play a note as the filter is all the way closed with zero envelope tracking.
Now take a modulation slot, and have the Source be "Filter Env." Set the Amount to 100. Set the Destination to "Filter 1 Frequency." You should be able to hear notes again, as we have set the mod matrix to basically emulate the "Env" knob. *Now do this same thing in a second slot. Same source, same destination.* Now, with the Amount still at 100 in the *first* slot, slowly increase the Amount in the second slot while playing notes. Notice how the filter clearly opens a little more even with a mod slot already claiming to push "100%" value to the filter? Set the "Filter Env" sustain to the maximum so that the filter stays static instead of decaying. You will notice that it takes two modulation slots (or a "Double Destination" mod slot with both destinations pointing to the same parameter) in order to push a target to its maximum value. Try this with LFO's as the modulation source as well, and different destinations.
(The reason that we are making use of the Mod Matrix instead of just using the Filter Envelope to do what it already does is to demonstrate what I'm saying - the "Amount 100" doesn't transmit the peak value that a source can actually generate. When building new sounds, suddenly you notice that you aren't getting the peak value from the modulation source as you might think...)
And note that pushing 0-100% in integers will produce truncated or rounded values when trying to map it to a target that actually goes 0-127.
I have developed workarounds for this, but it's an oddity in the programming that really could and should be a little cleaner. But with that being said, if you get creative in the Thor Mod Matrix, and really get wild with it inside of a combinator and use the CV splitter, you can push things well out of range from a control perspective (the Free LFO Rate can be pushed beyond the range of the actual rate knob in both directions for example...) and it can make for some interesting tricks and effects ;)