Unable to reproduce the issue on win-10 and ubuntu 17.10 using chrome reported version #70.0.3538.67 and latest chrome #72.0.3592.0.
Attached a screen cast for reference.

Following are the steps followed to reproduce the issue.
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1. Used extension https://chrome.google.com/webstore/detail/do-not-close-browser-with/iiolkehjeklhkdphaakkceadenbcdahj and added to chrome.
2. Set chrome to "Continue where you left off".
3. Closed the last tab of the window by clicking the close button on the topmost right corner.
4. Opened Chrome again.
5. Observed that the last closed tab did not get restore and opened the chrome welcome page as the last tab.

reporter@ - Could you please check the attached screen cast and please let us know if anything missed from our end. Also please check the issue on latest chrome #72.0.3592.0 by creating a new profile without any apps and extensions and please let us know if the issue still persist or not.

Thanks...!!

Deleted: 899078.mp4 937 KB

	899078.mp4 937 KB View Download

There are several things that are wrong in the screencast, so here a more comprehensive list of steps to reproduce. I just went through them on Linux:

 1 open Chrome with a fresh profile (I ran $ google-chrome --user-data-dir=/tmp/chrome_profile)
 2 go to chrome://settings/ and enable "Continue where you left off"
 3 install https://chrome.google.com/webstore/detail/vimium/dbepggeogbaibhgnhhndojpepiihcmeb
 4 open facebook.com, close all other tabs, so facebook is the last one open
 5 make sure you have not focused an input field and type x - vimium will call tabs.remove and close the tab which will also close the window
 6 reopen Chrome with the same profile (again $ google-chrome --user-data-dir=/tmp/chrome_profile)
 7 Chrome opens and the tab with facebook got restored - this is wrong, it should be an empty tab
 8 steps 5-7 can be repeated as often as you want, it's not that facebook gets only restored the first time the tab is closed
 9 now if you close the tab using Ctrl-w, the window closes
10 if you reopen Chrome with the same profile, Chrome opens with one empty tab - this is the right behaviour and it should be the same when using the webextension API, but as seen in steps 5-7 it isn't

Thank you for providing more feedback. Adding the requester to the cc list.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

As per comment #3, Able to reproduce the issue on reported chrome 70.0.3538.67 and latest chrome 72.0.3595.0 and issue not seen on M-60 Using Ubuntu 17.10. Hence, Marking it as Untriage and will provide Bisect info and other OS behavior soon.

Thanks...! 

Able to reproduce the issue on the reported chrome 70.0.3538.67 and latest canary 72.0.3595.0 using Ubuntu 17.10.Below is the bisect information for same.

Bisect Info:
================
Good build: 68.0.3427.0
Bad build: 668.0.3428.0

CHANGELOG URL:
https://chromium.googlesource.com/chromium/src/+log/9fedcd6889424af9766ebf07eab67d42ec0a9091..2969739effcde2fdba105d25d8db903bdfdb5db0

Suspect: https://chromium.googlesource.com/chromium/src/+/2969739effcde2fdba105d25d8db903bdfdb5db0

Reviewed-on: https://chromium-review.googlesource.com/1045790

erikchen:Please confirm the issue and help in re-assigning if it is not related to your change. Issue not seen on Mac and Windows.

Thanks..!