How would berlin take in the catholicized native populations, in regions with such groups?
They would be treated as every other christianized native population whereever on the globe tegradless the provenance of the missionaries : catholic, reformist, anglican, methodist, lutheran, baptist ...
IMHO a rather unneccessary question.
In short :
From 1900 onwards anti-catholicism had NO political effect AT ALL.
Long(er) :
It seems often forgotten here around
(i.e. also in discussing possible affiliation of parts of Austria to Germany) that the "Kulturkampf" started to end with the first Anti-Socialist Laws by Bismarck 1878 and actually ended in 1882 with diplomatic relations between Germany, Prussia and the Vatikan resumed.
1887 the pope Leo XIII even declared publically
the "Kulturkampf" as
ended.
At least from the midth 1890ies there WEREN'T any such anti-catholic animosities to speak of.
... not more animosities as there might be between Welsh and Glaswegians, Friesians and Badenians, East-Prussians and Bavarians ... i.e.
The sometimes opposition of the (
mainly catholic coined) Zentrum party was that of one of many political parties, as i.e. the different conservative parties as well.
The Zentrum gained historically its position due to the attempted oppression working as "well" - or rather advertising - as the later Anti-Socialist-Laws only helping the SPD to rise to its allembracing 'subculture' and political weight for which the catholic Zentrums parts was shining paragon.
What should have beenand should be taken as an example all around the times and places that oppression DOES NOT WORK and only helps the oppressed opponent.