Hi,
doing manipulations on client side while setting up web app is a weird thing.
But I faced the same problems.
Some of them are declared in this thread:
https://communities.ca.com/thread/241730209
If you have test environment you may try to define X-UA-Compatible as IE8 or EDGE (IE8 is a first of Internet Explorers which supports CSS2 correctly which is enough for regular things).
<meta http-equiv="X-UA-Compatible" content="IE=edge, chrome=1">
OR
<meta http-equiv="X-UA-Compatible" content="IE=8">
To make that meta works correctly it should be defined in frameset page and also in each frame.
Hope this makes IE11 work as regular browser without any clientside manipulations.
Regards,
cdtj