If I may attempt to paraphrase:
"You" are not "your thoughts": you are the watcher of your thoughts.
"You" are not "your thoughts": you are the watcher of your thoughts.
All "mental stuff" is mediated by three aspects i.e. 1) Intellect (aka Buddhi), 2) Ego/Self-Identity (aka Ahamkara) and 3) Sensory Mind (aka Manas). It is in the teasing out of all mental stuff into these aspects as being completely independent of "Consciousness" (aka Purusha) that is to be understood and practiced. In "normal life" Consciousness is bound to the above three aspects of "mind" and hence "suffers bondage". Patanjali Raja Yoga follows on Samkhya by giving a eight-part framework/discipline (aka Ashtanga Yoga) to literally "stop all mental/thought stuff creation/expansion". Then Consciousness is no longer bound to externalities (including its own "mind") but becomes settled within itself which is called Liberation (aka Moksha).
The Samkhya is Atheistic and Dualistic Realism and quite compatible with Modern Science where the former gives a "inside out" experiential and subjective model while the latter details a "outside in" material model.
This is not true. There are both theistic and atheistic branches in the Sāṁkhya school. It is a myth that Sāṁkhya is atheistic. In fact, Patanjali himself is in the theistic school of Sāṁkhya as he talks about: "īśvara praṇidhāna" in the sūtras and even defines īśvara.
Here's a fantastic lecture by Edwin Bryant discussing the Īśvara of Yoga Sūtras and Sāṁkhya in general: https://www.youtube.com/watch?v=SGXzTf6ZA-4
In Patanjali Yoga Sutras the concept of "God" is merely used as an entity and technique to help you in your practice to break out of your self-identity (i.e. Ahamkara). It is just one among a set of techniques. There is only half a dozen sutras which even mention god in the entire text (see this succinct translation by Bon Giovanni - https://sacred-texts.com/hin/yogasutr.htm). It is in the later commentaries on the text that you find an elaboration according to the pre-existing beliefs of the author.
You can turn it the other way round and the claim would be even more valid: Atheism came later in the Sāṁkhya schools. The scholars have a bias towards atheism so it's not surprising they'd claim that.
This is proven by the fact that the Mahabhārata's Bhīṣma-parva has a whole chapter on Mokśa-dharma which give us the very first signs of a proto-sāṁkhya philosophy and it is very much theistic. Also, the later added atheistic Kapila philosophy is a deviation from the original Kapila, the avatar of Lord Viṣṇu.
Even Patanjali is mentioned as Śeṣa in the scriptures and every school agrees with it. Śvetāśvataropaniṣad is one of the earliest references to Sāṁkhya and is very much theistic. Sāṁkhya being atheistic is a fiction. There were atheistic Sāṁkhya branches but it was never 'only' atheistic.
> "God" is merely used as an entity
That is true, because Patanjali's project was "svarūpe avasthānam", the method by which the seer can abide in its own nature. Īśvara is merely used as a prop to gain something else, which is okay because that is what Yoga Sūtra is about but it does not mean Sāṁkhya was originally atheistic or that theistic Sāṁkhya is a later addition.
No, current scholarship is unanimous in accepting that the Atheistic view came first. Unless some new unknown texts come to light to make us revise the dates that is what we have to live with.
Outside of the classic sutra texts mentioned above, there is only the "Kapilopadesha" from the Bhagavatha Purana and "Kapila-Gita" from the Mahabharatha which seem to espouse proper Samkhya philosophy. All other mentions in the upanishads/vedas/puranas/itihasas seem to be just a mention without any substantial details.
The Historical Development section gives a good overview - https://en.wikipedia.org/wiki/Samkhya#Historical_development
To say something is not necessary doesn't entail that it's doesn't exist or that it's philosophically untenable.
Śankara does debate with atheistic Sāṁkhya so I'm not saying that it's not the case but it's a mistake to claim that Sāṁkhya is non-theistic because that's what some authors write when it's not the case. The majority of Sāṁkhya traditions were īśvara-vāda, theistic.