"can a Christian or Muslim be also a brāhmaṇa, kṣatriya, etc., based on the guṇas they acquired during the course of their life?"
As already stated in Gita, the classification is decided based on the nature. It is not related to ethnicity. The 4 classes are ever existent irrespective of religions.
BG 18.41 - O scorcher of enemies, the duties of the Brahmanas, the Ksatriyas and the Vaisyas, as also of the Sudras have been fully classified according to the virtues born from Nature.
-- Gambhirananda translation
There is no reference of whether only a certain group of people can be part of these 4 classes.
"For example, can a learned man and a practicing Muslim like the former/late President of India A. P. J. Abdul Kalam be called a brāhmaṇa?"
Coincidentally I have taken Dr. Kalam's reference as Brahmana in this answer. I will categorise Albert Einstein also in the same category. See my answer in: Who becomes a Brahmin?
Abdul Kalam had all, what it takes to become Brahmana. Started from a very humbled background (Shudra), who used to petty jobs. He was sincere and knowledgeable in his field (Brahmana). Publicly he was Never behind money (Vaishya) or fame (Kshatriya). Being bachelor throughout the life, he could have been on the path of Brahmacharya. He had love for children and always thought well about his country.
"the 4 four varṇas are present in all individuals?"
Like how anyone cannot escape 4 directions (north/south, east/west), every individual will fall under these 4 classes without fail.
Sometimes due to inter-class marriages, certain sub-classes of these 4 classes are created. However these sub-classes are just fine-tuning of the original 4 classes. More information here:
What are the order & duties of the children born from intermixing/hybridisation of 4 classes?
"can a brāhmaṇa behave like śūdra at times and vice versa?"
During lifetime, people may choose to alter their Swa-Dharma. e.g.
- Mahatma Gandhi was born & worked according to Vaishya division; However at later point of his life, he acted like a Brahmana [read BG 18.42]
- Drona/Ashwathama were Brahamana, but fought on behalf of Hastinapur as of they were Kshatriyas; Similarly Krishna was born & brought up into Vaishya division, but lived life as Kshatriya