You see this in other places too. (American Irish Catholics are more conservative than modern Irish Catholics, for instance.)
With muslim guestworkers arriving in the 50's it was clear that theses guests weren't staying for long and subsequently a) muslim religious institutions weren't (for a long time) included in this "state-collects-the-moneys"-Scheme and b) thus it was welcomed that they'd be financed and run by foreign institutions.
In the result you typically have mosques that are either exclusive on grounds of ethnicity (eg the mosques run by the turkish state)* or inclusive on grounds of the interpretation of islam (sadly the Saudi funded radicalist ones are very inclusive).
* since interpretation often is a cause of dispute within regions you can have more inclusive interpretations like the Alavites that are usually ethnically homogenic.
That a foreign nation runs Churches in a sovereign state is really laughable. It's of course always a means of political influence and thus what Saudi Arabia and Turkey does is directly comparable to what the Catholic Church did until the "Papal States" were dissolved.
There's actually an organized Muslim church in two states (Ahmadiyya Muslim Jamaat) that has managed to fulfil the requirements but they represent a minority sect (i.e. not Sunni or Shia -- approximately 35k members in all of Germany).
There's nothing preventing e.g. Sunnis from forming such an organisation, really.
I believe, but correct me if I'm wrong, it's precisely that they are often foreign run/influenced. If interpretations cause conflicts, these conflicts usually run along state lines (ie. Iran/Turkey). This plus language barriers (arabic vs. turkish vs. farsi etc.) create incentives to not be inclusive.
But I only said there wasn't anything from a legal perspective stopping them. If the various sects fail to cooperate with each other in ways that prevent them from fulfilling the requirements, that's on them, not on the government. It's not xenophobia, just old-school sectarian disputes.
For example the Evangelical church (EKD) is a federation of mostly Lutheran and reformed/Calvinist churches and they managed to agree on enough points to organize beyond their sectarian boundaries. But there are of course a lot of Evangelical or "free" churches that are not part of the EKD (nor affiliated with the Catholic church) and they of course don't get the same status.
The problem with understanding Muslim sectarianism in the West seems to be that we're so ignorant that we chalk about anything outrageous to religious differences with Christianity that we don't recognize basic distinctions like Islam vs Islamism, thinking any criticism of the latter would be a form of hostility to the former. We lump all "Muslims" together in one group (which some Muslim groups certainly know to use to their advantage) and then get confused when we find out they hate each other's guts (much like Protestants and Catholics have for a long time).
I guess there is hope the influx helps to rejuvenate and ground the expat Syrian culture.
Integration into the German society on the other hand is also a critical. Labeling does not help people to feel integrated and to step forward when needed. Like a few weeks ago when a terrorist cell with a bomb maker was found due to actions from that community. That took guts and trust from their side.