Origin of transliteration of ~j/sw to ~r in Mandarin In Malaysia/Singapore, “Raja” is often transliterated to 拉惹，although Wikipedia uses 拉者as the name for its article on the title.
e.g. Ayer Rajah 亚逸拉惹
Perlis’s Raja 玻璃市拉惹（https://zh.m.wikipedia.org/zh-sg/%E7%8E%BB%E7%92%83%E5%B8%82%E6%8B%89%E6%83%B9）

拉惹勒南 Rajaratnam
惹兰 (Jalan) also frequently appears in street names. Why is 惹 used to transliterate ~ja other languages?

On a perhaps unrelated note, why is 瑞 in 瑞士 and 瑞典used to transliterate the ~sw/su in Swiss or Sweden?

Were 瑞/惹 read something like sw/ja respectively in a more popular dialect of Chinese when such transliterations were standardised? Are there other examples of transliterations into Chinese reflecting dialectal pronunciations (e.g. 麦当劳 McDonald’s?)
Yes. 

瑞 is seoi6 (IPA: /sɵy̯²²/) in Cantonese, and sūi (IPA: /sui²²/) in Hokkien, so is a fairly close match to the French word Suisse and the English name for Sweden. The origin of a lot of translations for smaller Western countries came from the Chinese varieties of the southern ports of Guangzhou (Canton) and Xiamen (Amoy) amongst others.

惹 in some varieties of Hokkien (specifically Zhangzhou, which gave rise to Penang's variety) is pronounced jiá (IPA: /d͡ʑia⁵³/), which again is a closer match to the voiced affricate of -ja ज in Sanskrit-derived Indo-Aryan languages. 

The 者 version is one option that Mandarin has (being an affricate, and in right area of the mouth), and also has the right semantic connotations (representing a person).

Although it is not a general phenomenon, topolectally-divergent transliteration is still a thing. Compare how Mainland Chinese, Malaysians and Singaporeans transliterate David Beckham's surname (貝克漢姆, simpl. 贝克汉姆) with how Hong Kongers/Macanese do so (碧咸), with how Taiwanese do so (貝克漢).