It's better to file feedback like this on the bug tracker (
https://crbug.com/pdfium/new). That said, there are a number of known issues in PDFium around performance in specific cases like this; feedback and additional data is always welcome, but there isn't necessarily going to be a quick fix.
The section in the PDF specification that you're quoting doesn't really have to do with performance, but precision. Implementations with more complex handling of transparency can reduce loss of precision by performing intermediate operations at higher precision, but rasterization to the final output device still has to occur eventually.