You just quoted the line prohibiting the forcible transfer of protected persons **OUT** of occupied territory. That, of course, has nothing to do with the transfer **IN** of citizens of the occupying power. That's covered by the last line of Art 49: "The Occupying Power shall not deport or transfer parts of its own civilian population into the territory it occupies." NOTE: that line says "transfer", and not "forcible transfer" i.e. colonizing occupied territory with your own citizens is UNCONDITIONALLY prohibited.
First refugees travelling on Hungarian bus arrive at Austrian border (Reuters)
from the article: Israel policy allows settlers to rampage unchecked