Epub is epub and devices are devices. With iPad ignoring text-align: center; there is a lot of extra work going on out there to put in substitute elements to make ePub work with devices. Every new device presents new "challenges".
The most common hack to overcome this iPad problem is to introduce a blank <span> statement into the paragraph. It can be a lot of work and looks like this:
<p class="center-me"><span>I am text that wants to be centered</span></p>
We use a lot of dedicated class statements in headers and other text to get good looking outputs. here is our generic title block structure:
<p class="title-sub">The sub-title</p>
<p class="title-author">The author of the work</p>
<p class="title-contributor">Any old contributor</p>
<p class="title-other">For any other text that may be required</p>
So with that little combination, the iPad doesn't center text when justified mode is on.
Something like this goes in the OPF manifest:
This goes into the <head> of each page:
Feel free to crack the ePub open and have a look.
Save this into a file insertSpan.js (or whatever). If you minify it, it is a whopping 800Bytes.