Unable to reproduce the issue in Mac 10.12.2 by using chrome reported version #56.0.2924.28 and latest canary #57.0.2962.0.

Steps followed to reproduce the issue are as follows:
-----------
1. Enabled: System Preferences > Trackpad > Scroll & Zoom > Smart zoom
2. Opened a PDF
3. Double-tapped with two fingers.
4. Observed that the PDF content zoomed as expected.

Attaching screen cast for reference

jleedev@ - Could you please check this issue on latest canary #57.0.2962.0 by creating a new profile without any apps and extensions and please let us know if the issue still persist or not.

Thanks...!!

Deleted: 676668.mp4 19.0 MB

676668.mp4 19.0 MB Download

At 0:15, the toolbar on top is cropped on the right side.

I confirm existence of the issue.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/b0de2c52754fe0f4978fe59c36d560f921375e31

commit b0de2c52754fe0f4978fe59c36d560f921375e31
Author: Kevin McNee <mcnee@chromium.org>
Date: Mon Aug 28 17:17:54 2017

Disable smart zoom for PDF viewer.

On Mac, the smart zoom gesture (double-tap with two fingers on Mac
trackpad) changes the page scale. This is undesirable because it scales
the viewer's controls off screen.

Now, in Browser::PreHandleGestureEvent, we drop the kGestureDoubleTap
event (which is created from NSEventTypeSmartMagnify) when we have a
PDF viewer.

Bug:  676668 
Change-Id: Ic523693ba6bed71460944d77a0a132a69ca737e3
Reviewed-on: https://chromium-review.googlesource.com/614084
Reviewed-by: Scott Violet <sky@chromium.org>
Reviewed-by: dsinclair <dsinclair@chromium.org>
Commit-Queue: Kevin McNee <mcnee@chromium.org>
Cr-Commit-Position: refs/heads/master@{#497784}
[modify] https://crrev.com/b0de2c52754fe0f4978fe59c36d560f921375e31/chrome/browser/pdf/pdf_extension_test.cc
[modify] https://crrev.com/b0de2c52754fe0f4978fe59c36d560f921375e31/chrome/browser/ui/browser.cc

Smart zoom is now disabled for the PDF viewer, so it no longer scales the viewer's controls. As for having the viewer handle the gesture, see crbug.com/757541.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/6ce83ed8a96c2a8e96931ce84c785837c1b9e7ee

commit 6ce83ed8a96c2a8e96931ce84c785837c1b9e7ee
Author: Kevin McNee <mcnee@chromium.org>
Date: Tue Oct 16 14:38:30 2018

Remove hack to disable double-tap to zoom gesture for PDF viewer

This effectively reverts
https://chromium-review.googlesource.com/c/chromium/src/+/614084
which added this hack.

This is no longer necessary as wheel listeners can now prevent the
double-tap to zoom gesture (see  issue 802369 ) and the PDF viewer has
the necessary behaviour already (see testPreventNativeZoomFromWheel in
gesture_detector_test.js).

Bug:  676668 ,  802369 
Change-Id: I4cb840d9f383c0f8aa4a47851d749de41004816b
Reviewed-on: https://chromium-review.googlesource.com/c/1281172
Reviewed-by: Scott Violet <sky@chromium.org>
Reviewed-by: dsinclair <dsinclair@chromium.org>
Commit-Queue: Kevin McNee <mcnee@chromium.org>
Cr-Commit-Position: refs/heads/master@{#599975}
[modify] https://crrev.com/6ce83ed8a96c2a8e96931ce84c785837c1b9e7ee/chrome/browser/pdf/pdf_extension_test.cc
[modify] https://crrev.com/6ce83ed8a96c2a8e96931ce84c785837c1b9e7ee/chrome/browser/ui/browser.cc