They are reading it backwards. The amendment:

...  to ensure that the ability of users to access or distribute lawful content or to run lawful applications and services of their choice is not unreasonably restricted.

I.e., this asks for regulation to prevent restriction to the running of lawful applications.

The commentary:

Free Software is not compatible with standards used to try to restrict the run of a « lawful application »

but trying to restrict the running of a "lawful application" is what the amendment wants to prevent.

The amendment says nothing about preventing the use of unlawful software (including modified lawful software), it only mentions that the use of lawful software should not be restricted.

The amendment:

Member States shall ensure, subject to paragraphs 2 and 3, that no mandatory requirements for specific technical features, including, without limitation, for the purpose of detecting,intercepting or preventing infringement of intellectual property rights by users, are imposed on terminal or other electronic communication equipment

Aren't they asking that no such requirements are imposed?

But I don't know. TBG reacted to this particular text by saying it appeared to by hysterical. Not to speak of the fact that it hasn't been tabled for July 7.

When the capital development of a country becomes a by-product of the activities of a casino, the job is likely to be ill-done. — John M. Keynes