This reproduces reliably on new tab.
It sometimes reproduces even when switching to an existing new tab.
It doesn't seem to happen when opening about:preferences or about:addons in a new tab.

The unexpected modification to the primary selection on new tab happens with this call stack on revision adc59d50adf8:

0 _on_select(event = [object Event]) ["resource:///modules/UrlbarInput.jsm":1425:20]
this = [object Object]
1 handleEvent(event = [object Event]) ["resource:///modules/UrlbarInput.jsm":333:22]
this = [object Object]
2 select() ["chrome://global/content/bindings/textbox.xml":107:26]
this = [object XULElement]
3 UrlbarInput/thismethod ["resource:///modules/UrlbarInput.jsm":115:35]
4 focusAndSelectUrlBar() ["chrome://browser/content/browser.js":2428:10]
this = [object ChromeWindow]
5 _adjustFocusAfterTabSwitch(newTab = [object XULElement]) ["chrome://browser/content/tabbrowser.js":1186:8]
this = [object Object]
6 updateDisplay() ["resource:///modules/AsyncTabSwitcher.jsm":440:26]
this = [object Object]
7 postActions() ["resource:///modules/AsyncTabSwitcher.jsm":618:9]
this = [object Object]
8 queueUnload(unloadTimeout = 300) ["resource:///modules/AsyncTabSwitcher.jsm":1026:9]
this = [object Object]
9 requestTab(tab = [object XULElement]) ["resource:///modules/AsyncTabSwitcher.jsm":1015:9]
this = [object Object]
10 updateCurrentBrowser() ["chrome://browser/content/tabbrowser.js":917:28]
this = [object Object]
11 _setupEventListeners/<(event = [object Event]) ["chrome://browser/content/tabbrowser.js":4509:13]
12 set selectedIndex(val = 1) ["chrome://global/content/elements/tabbox.js":193:11]
this = [object XULElement]
13 set selectedPanel(val = [object XULElement]) ["chrome://global/content/elements/tabbox.js":207:4]
this = [object XULElement]
14 set selectedIndex(val = 1) ["chrome://global/content/elements/tabbox.js":532:8]
this = [object XULElement]
15 set selectedItem(val = [object XULElement]) ["chrome://global/content/elements/tabbox.js":551:32]
this = [object XULElement]
16 set selectedTab(val = [object XULElement]) ["chrome://global/content/elements/tabbox.js":86:8]
this = [object XULElement]
17 set selectedTab(val = [object XULElement]) ["chrome://browser/content/tabbrowser.js":261:4]
this = [object Object]
18 loadOneTab(aURI = "about:newtab"

_gBrowser.updateCurrentBrowser calls requestTab before setting _selectedTab and "Update the URL bar".

The location bar contents are subsequently updated at

0 _setValue(val = "", allowTrim = true) ["resource:///modules/UrlbarInput.jsm":767:4]
<failed to get 'this' value>
1 set value(val = "") ["resource:///modules/UrlbarInput.jsm":749:16]
<failed to get 'this' value>
2 URLBarSetURI( <Failed to get argument while inspecting stack frame>
updatePopupNotifications = true) ["chrome://browser/content/browser.js":2847:2]
<failed to get 'this' value>
3 onLocationChange( <Failed to get argument while inspecting stack frame>
aRequest = null <Failed to get argument while inspecting stack frame>
, aFlags = 0, aIsSimulated = true) ["chrome://browser/content/browser.js":4895:6]
<failed to get 'this' value>
4 callListeners( <Failed to get argument while inspecting stack frame>
<Failed to get argument while inspecting stack frame>
) ["chrome://browser/content/tabbrowser.js":742:28]
<failed to get 'this' value>
5 _callProgressListeners(aBrowser = null, aMethod = "onLocationChange" <Failed to get argument while inspecting stack frame>
, aCallGlobalListeners = true, aCallTabsListeners = false) ["chrome://browser/content/tabbrowser.js":755:6]
<failed to get 'this' value>
6 updateCurrentBrowser() ["chrome://browser/content/tabbrowser.js":965:9]
<failed to get 'this' value>

This ordering dates back to at least "Tab switch refactoring".
https://hg.mozilla.org/mozilla-central/rev/564a9e11d9ec89b0d9a6e2ea7e93cd531c9a468d
I don't know whether this was the ordering at the time of https://hg.mozilla.org/integration/autoland/rev/562966f195b0 triggering this regression. I haven't identified how that triggered this regression.

The intention of UrlbarInput._on_select() is to adjust the primary after it has been set (differently) by the editor. The editor does not set the primary during HTMLInputElement::Select() as used by focusAndSelectUrlBar(), and similarly _on_select() should not adjust the primary in this situation.

I also investigated changing focusAndSelectUrlBar() to merely focus and not select the urlbar, but selection is expected at least on keyboard shortcuts to directly focus the location bar.

This suppresses modification of the primary selection when opening a new tab
as well as when a keyboard shortcut is used to directly focus the location
bar.

Depends on D37353

https://treeherder.mozilla.org/#/jobs?repo=try&tier=1&revision=db89e8caa917fb96e97a8eaf019ed585007afba3

@karlt thanks so much for working on this! I'll be much happier once this is fixed.

https://hg.mozilla.org/mozilla-central/rev/435cbd9fb896
https://hg.mozilla.org/mozilla-central/rev/3cf34ed0ac83

Is this something you wanted to nominate for Beta approval or can this ride the trains?

This has existed long enough that I think there is no urgency to uplift, thanks. 69 is also not an ESR so no benefit there.
There would be a small risk to uplift with some of the refactoring that has been happening, and so safer to ride trains.