I wonder if the author has protested at any point (getting into an unmarked vehicle, not being returned to original destination, being ordered to take the clothes off (!?)). I also wonder if he was formally informed of the reason behind the detainment.
And finally: if ever faced with such a situation, does a person have the right to a) record everything that happens on the phone (including faces of the police officers + audio), and b) if asked to stop, would it be ok to say "i have the right to record all you do" or something similar?
To my knowledge, you are allowed to record the police. There was a sentence by the highest German court just a few weeks ago, stating that the police is not allowed to ask for ids of protesters recording them [0].
You generally have quite a few rights at police checks. For example, you are allowed to decline a breath test. The problem with these rights is, that you lose time if you exercise them, because they will take you to the station. So they are not that useful in cases like this.
It is highly unlikely that the German police will beat you up or something like that, but you will have wasted some hours. Just be friendly and do not confess anything. Especially at traffic stops, they will ask you why they stopped you. Just say you do not know, because you do not have to incriminate yourself.
Criminal law (StGB in .de) and rules relating to proceedings in crime-related investigations (StPO in.de) are not harmonized in the EU, so no, there is no EU law for this.
not much. EU hasn't got to the point to require strong citizen protections from law enforcement for whatever reason. UK is more similar to the US since uses a similar framework, but many accepted doctrines are quite different in EU even state by state, for example about the allowance of illegally obtained evidence
And finally: if ever faced with such a situation, does a person have the right to a) record everything that happens on the phone (including faces of the police officers + audio), and b) if asked to stop, would it be ok to say "i have the right to record all you do" or something similar?