Indeed, if you deny Location access to Android Chrome, you cannot then disable the Location setting in Chrome Settings, leading to annoying permission prompts.

I think the problematic code is around https://cs.chromium.org/chromium/src/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SingleCategoryPreferences.java?l=705&rcl=9ee27abfd52a6fc4951be5010f1ed884823d7c12

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/5ea0e6e86497b8e28e2b744f534128cf5f001308

commit 5ea0e6e86497b8e28e2b744f534128cf5f001308
Author: Kamila <hkamila@google.com>
Date: Mon Nov 19 15:25:43 2018

Allow the user to disable permission prompts when disabled in Android (behind flag)

1. Enables modification of the toggle of Chrome Site Settings permissions which can be managed
in Android. This is done in order for the user to be able to disable these permissions in
settings, even when access is not granted to Chrome in Android.

The permissions modified are:
- Camera
- Location
- Microphone
- Notifications

2. Changes the string and makes it appear only when the permission is disabled for Chrome, but
the user hasn't disabled the permission in Chrome. (as per comments in patchset 5)

---------
Images
---------
Before
In any case when location is blocked for Chrome in Android:
https://imgur.com/a/6r2MMan

After
Location Blocked for Chrome and in Chrome: https://imgur.com/a/wsXfrzL
Location Blocked for Chrome but "Ask" in Chrome: https://imgur.com/a/qiq3XTP

---------
Note
---------
This cl was initially intended just to change the UI for Location permission, but the change
makes sense for all permissions similar to Location. The initial image with only the location
change until patchset 5 was: https://imgur.com/a/WjHqUZu


Bug: 814106
Change-Id: Iefd929cf85f83a6f1dd3155c75875c2d3f66829d
Reviewed-on: https://chromium-review.googlesource.com/c/1275853
Commit-Queue: Kamila Hasanbega <hkamila@google.com>
Reviewed-by: Finnur Thorarinsson <finnur@chromium.org>
Reviewed-by: Christian Dullweber <dullweber@chromium.org>
Cr-Commit-Position: refs/heads/master@{#609301}
[modify] https://crrev.com/5ea0e6e86497b8e28e2b744f534128cf5f001308/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SingleCategoryPreferences.java
[modify] https://crrev.com/5ea0e6e86497b8e28e2b744f534128cf5f001308/chrome/android/java/src/org/chromium/chrome/browser/preferences/website/SiteSettingsCategory.java
[modify] https://crrev.com/5ea0e6e86497b8e28e2b744f534128cf5f001308/chrome/android/java/strings/android_chrome_strings.grd