I started this six days ago. Life changes.
It is unsurprising that the subject of persecution comes up in a discussion of Jewish genetics.
Distinctions need to be made. Bias against a group can go on at low level for years - maybe centuries - and no one much remarks on it, because everyone just accepts that's the way things are. Some people have this status in society, some have that one, but it's just normal life. All but the smallest societies are stratified, often much more than ours in some ways. When we think of the archaeology of burials, for example, think how our own will look. The stone markers will be different, but the clothing and burial objects of the rich and all but the very poorest are going to look similar in the US.
Persecution gets noticed when it is intermittent. The tone of outrage is often hugely "We thought we were accepted here. We thought you were our friends!" Modern girls look on the lives of women in the past and think "I would never put up with that." Sure you would. It was normal life. You would have the same focus and concerns as the women around you.* We put up with a lot because we don't really think of it s putting up with anything.
Permissions also change with class or group. In many places the elites have to hold to the official religion and keep up observances, but the peasants and poor in general have more minimal requirements. No one much cares what they do out in the provinces. Show up Christmas and Easter. Don't harm the sacred groves. Don't do anything obviously undermining the status quo.
If a population keeps growing in a region, how much are they being persecuted on an ongoing basis? There may indeed be status differences between groups, and they may be entirely unfair. Ingroups tend to set up some privileges for themselves everywhere. If you belong to this religion you can't marry into the nobility. Well, but how many people were marrying into the nobility anyway? Has there been a run on this? The Jews increased greatly in number once they entered the Rhineland. But we don't know this from historical records all that much. There is a gap of about a thousand years 500-1500 in historical information about Jews in Europe. They kept up a lot of writing about religious matters and then held tight to it, so we still have that aspect. And we are now figuring out from genetics and archaeology a lot of the missing pieces. So how do we know there were so many in the Rhineland? Because there were lists of the martyrs from the First Crusade. They show up in the historical record as persecuted badly. But that is likely because it was an exception, one more example of "But we have lived among you for years! We thought we had a place here!" Does that mean they were fully accepted members of that society? Not in the least. But whatever prejudices they had visited on them didn't rise to the level of being mentioned, and their population increased.
* The world where you go back there and refuse to put up with it and set a good example is more fantastical than the time travel itself. Yes, modern fantasy novelists like to set up stories like that, of girls trying to break out(!) of old ways and become a wizard, or a warrior, or a bard or some other previously forbidden role. (Tolkien and Lewis were early examples and did it well.) But that is largely a modern value.