Hi Jason,
As Saloua has mentioned the BOE web application now comes integrated for CMC, Launchpad, AnalyticalReporting, etc. which were all individual webapps in XI 3.1.
Manual modification to the BOE webapp is not supported.
However, you could also consider "splitting" the web applications. This separates the static content (served by an additional web server) and dynamic content (hosted on the web application server).
The size of the content deployed on each server reduces, and consequently the number of requests for static content do not reach the web application server and likewise for dynamic content on the web server.
Page 23 of the below guide explains this in detail:
Web Application Deployment Guide - 4.1 Support Package 3
This would require additional configuration, but addresses the concern of overheads, request handling and performance.
Hope this helps.
-Sid