Hmm... it works for me in that it doesn't throw an error...

...but to get it to work the way you want it to, you'll have to fix something. It won't cause the error, but TM won't work properly unless you change it.
Any inline roll in the embedded token-mod command line (or any plugger command) needs to be either deferred (so that it happens in the dispatched command), or it needs to be extracted so that the value is sent (using .value). I'll explain why in just a second, but this is the command that I dispatched to make the above output (and I watched it update bar2 of the selected token):
!&{template:npcdmg}{{description=They bite down hard dealing [[[[1d4]][1d4]+3]] piercing damage and absorbing $[[0]] Chakra}}{&eval}token-mod --set bar2|+$[[0]].value {&/eval}{&simple}
Note, too, I deleted the --ids argument from token-mod, because I obviously don't have a token with that ID. Also, with SelectManager installed, you can rely on that script to give back the selected token... so that's how I let it run: affecting the token I had selected.
Why You Have to Defer or Extract the Roll
What happens is that Roll20 has a turn at the command line before the message gets to the stack of API scripts. Roll20 processes the inline roll and adds the roll data to the message object that is being handed off from script to script. So... the original message has the original inline rolls.
Then the metascripts get a hold of that same message first (before normal scripts get a chance), and do what they need to do. In the case of Plugger, it sees that it has to send a secondary message. By the time it gets the command line that it will need to send (everything between the {&eval} syntax), the inline rolls that have been detected and parsed by Roll20 have been replaced with the roll markers: $[[0]]. But remember, the data for that roll is in the original message.
So when Plugger sends the command line, it sends the roll marker as part of the string of text. That command line gets parsed by Roll20 (looking for any new inline rolls, or sheet attribute calls, etc.), and then a NEW message object is created. Unfortunately, for a simple outbound command like that, Plugger can't (currently) pass on the original roll data that's in the original message... so what TokenMod sees when it gets the new message is a roll marker that *should* point to roll data, but there's no data there (it's in the original message).
That's why you want to extract the roll value before you send the command to TokenMod (so that TM only sees a value in that position in the command line), or you want to defer the roll until the TokenMod message is processed, so that the roll data is attached to the new message.
Specific to What You Are Trying...
All that said, I don't think you want to embed the roll in the TokenMod command line... because if the Roll20 parsers detect the inline roll formation, they are going to process it anyway as a part of the original message. There's no reason, in this case, to defer the roll until Plugger dispatches the TM command. The whole point to what you're doing is to be able to use a part of the roll you need in the outer command (the full attack value) as a component to the TM command.
If You Still Have an Error
Like I said, I couldn't produce that same error, so if you still get an error after you apply all of this advice to what you're trying to do, share your full command line. If I still can't replicate it, maybe your GM can invite/promote me and I can jump in the game and poke around, see if I can figure out what is going on.