The "inline_images" filter applies only to images below a configurable threshold size, 3k by default. I think saving the web page should work fine with that. Not sure why they were missing for you.
You can also right-click "save image as..." on inlined images. However, they will be downloaded in whatever format they were transcoded to, which might be webp.
You can disable specific features of mod_pagespeed fairly easily. For those two:
ModPagespeedDisableFilters inline_images
ModPagespeedDisableFilters convert_jpeg_to_webp