Very similar issue with WebGL and new input system, has been the case since early July.
All clickable areas using the new input system + UI Toolkit are offset relative to the top-left corner of the browser window instead of the canvas. So moving the canvas breaks the UI completely (e.g. can’t center it in CSS or use non-uniform scaling).
What you’re describing appears to be this issue, present since B1;
My issue has been placed under another bug (Unity Issue Tracker - [WebGL] Mouse position is not relative to the canvas when using the new input system) so there’s no way to really track the progress of -that particular- part of the bug or if both are related. Latest Input System version will not fix it, QA confirmed it has to be fixed in-editor code.
I tried re-reporting it here: (Case 1357476) Input detection is detected relative to browser size instead of canvas size in WebGL
Been told by @LeonhardP that we can ‘expect’ a fix to land in B10. Fingers crossed as this has been a blocker for any WebGL projects that want to use 2021.2, and 2021.2 is -the- WebGL upgrade version we’ve been waiting for years!