Why are there no online stores that sell manga in PDF format for the English translation? I have bought a copy of One Piece, but I have to use some apps to read that while I have bought it with a full-priced. For example, I bought a manga online on some random online bookstore. The price for the digital version of that manga is about $7, and for the physical version, it costs $10. 

It's understandable/acceptable for the price, with $3 different, because probably it was a cut-off from the printed cost which is come from the printed version, the digital version is print-less...

However, why do I have to read manga on some apps that were used for reading manga online? Why can they just give us, customers, the PDF version of the manga?
As a PC guy that uses spare time to research on DRM, I can tell you that PDF (Portable Document Format) sucks at protecting content in redistribution (in any form including printing, copying, uploading, etc.). There are two reasons: 


PDF is made for an easy exchange of document without worrying compatibility between different writing software 
there are no (as far as I know) universal DRM solution for PDF. Adobe DRM won't work on PDF-XChange Reader and vice versa. Some of them use customized PDF format which only specific application could read, thus limits the portability.  


In publisher's perspective, the second point is the thing that they don't want to see: bypassing DRM protection. As PDF properties, it becomes the less ideal media. To protect their revenue and IP, they're more willing to use a custom proprietary format because the benefits it provides outweighs the drawbacks.

Source:


The History of PDF (Paragraph 3, 2017)
Adobe Digital Edition uses ACSM file (a customized XML) with resource IDs inside rather that actual content. Other application couldn't get the content except ADE. (Adobe Digital Edition)
There are tools to remove ADE protection and convert them into plain PDF or EPUB. I won't post a link so please Google yourself.