Given that size that some gunneras, e.g. G. manicata can get to (10' x 10' easily) they must have a very big root system, especially as it can hold the plant up in boggy soil. So, yes, maybe you are right to be worried. I'm guessing here, but I think it would be more likely to push the liner up rather than pierce it (unless there's already a small crack in it). Either way, not good, so maybe you're doing the right thing keeping them in pots.
the roots are very much more "fleshy" than "woody" so I can't see much risk of damage, although the whole "crown" expands in time and , from experience, they're a nightmare to move once they get big.
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