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For me, patching is essential. I use a lot of patches (over 20).
Some people prefer KOReader to the native reader; I don't. YMMV.
As to your questions:
It's generally agreed that KOReader is better for PDF files than the native reader. I don't read PDFs, so I can't comment on it.
The book with the invisible text obviously has some color coding in its css. That can easily be removed with an epub editor (Sigil or the Calibre editor). Personally I edit all my ebooks, adjusting the formatting to my liking.
You can install and use custom dictonaries, but not use several of them at the same time. It's easy enough to hop between them, though.
Series and collections can be managed fully automatically with Calibre, with no manual work on the Kobo at all.
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