I've attached my Modify Epub settings. Yes, they're different from yours. But, I can't see anything that would stop it from removing those Google Play page maps (again, I've tried all combinations of those two checkboxes). I've also included the top of one of the pages with the play map on it and the Modify Epub log for the run.
EDIT 1: I was also wondering if it might be an epub3 thing. But, since your files are xhtml, I'm assuming that book that you used is also an epub3 (just like the one I'm using).
EDIT 2: And, I've just made another two runs with your first and second set of settings. No difference.
Code:
<?xml version="1.0" encoding="utf-8"?>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops" lang="en-us" xml:lang="en-us">
<head>
<title>Chapter 1</title>
<link rel="stylesheet" type="text/css" href="css/style.css"/>
</head>
<body>
<a id="GBS.0007.01"/>
<section role="doc-chapter" epub:type="chapter">
<h3>Chapter One</h3>
<div class="chapquote">
...
Code:
Modify ePubs version (1, 8, 1)
Logfile for book ID 1969 (Fixer Redux / Gene Doucette)
Job details 1969
Modifying: C:\Users\Dave\AppData\Local\Temp\calibre_46q9x9yr\yj1641ug_modify_epub\1969.epub
Updating metadata and cover
Parsing xml file: OEBPS/volume.opf
Parsing xml file: toc.ncx
Looking for redundant entries in manifest
Looking for unmanifested files
Looking for broken links in the NCX
ncx name: toc.ncx
Looping over ncx entries
Looking for Adobe xpgt files and links to remove
Looking for pagemaps
Looking for Google Play pagemaps
Looking for Adobe DRM meta tags to remove
Looking for legacy jackets
Adding or updating jacket
Current jacket removed: OEBPS/jacket.xhtml
Manifest item removed: jacket.xhtml (calibre_jacket)
Spine itemref removed: calibre_jacket
Manifest item added: jacket.xhtml (calibre_jacket)
Spine item inserted: calibre_jacket at pos: 1
Looking for html pages containing only broken image links
Looking for non dc: elements in manifest
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Removing child: {http://www.idpf.org/2007/opf}meta
Looking for html files to remove charset meta tags/encode to utf-8
Looking for embedded fonts
Looking for css @font-face style declarations
Looking for inline @font-face style declarations
Looking for CSS margins
Looking for inline javascript blocks to remove
Looking for .js files to remove
Stripping Kobo remnants
Looking for files to remove: ['iTunesMetadata.plist', 'iTunesArtwork']
Looking for files to remove: ['META-INF/calibre_bookmarks.txt']
Looking for files to remove: ['.DS_Store', 'thumbs.db']
Looking for unused images
Stripping spans
ePub updated in 0.44 seconds