This is probably challenging, but required nonetheless.
Special:CX works at the target wiki and applies its styles to both columns. This may make things in the source column look wrong. Here's just one example:
Here I am translating from English to Hebrew. The rows in the English infobox are aligned to the right because this is the Hebrew Wikipedia, but it should use the style from the source wiki as much as possible.
RTL is not the only issue here. Here's how the box looks in the source wiki:
Notice the horizontal lines that separate the sections—they don't appear in the translation interface. There are more issues, of course.