I'd like to purchase the original Japanese manga in digital form but prefer in PDF format as I don't want to be tied down to using a particular website or even losing my purchased manga (I remember buying a digital manga a couple years ago but when I logged into my account recently it was no longer there.)
As far as I know, there are no raw, digital manga being sold in PDF format. You can convert them, however, using applications found in the Internet. Here are some sites I found that sell raw, digital manga (and there are more mentioned in the forum links I posted below):
Where I found those sites above:
Japanese DLsite provides few Japanese manga in DRM-free PDF formats. The files can be downloaded and opened freely without any additional restriction.
The following search is for "Safe-For-Work" (as per their definition) manga; this excludes doujinshi and R-18 works but includes tankobon (単行本), magazine/anthology (雑誌/アンソロ), short story (短編), per-chapter (単話), and free-reading trial/demo (無料お試し版).