LSB == NBG
First of all, the Linux Standards Base is a crock. It only exists in the first place to allow people to write closed-source software and expect it to be able to run on a GNU/Linux system. LSB is about putting certain files in certain places so pre-compiled binaries can find them where they were told, thereby removing the need for the user to have access to the source code for the purposes of compile-time configuration.
Ordinarily, you can put *any* file *anywhere* -- that's what the "configure" step of installing a generic .tar.gz package is all about. "configure" generates a makefile which instructs the compiler as to where various required files are located and where to put the compiled binaries and libraries. "make" actually builds the binaries and libraries, though it doesn't move anything to its eventual location. "make install" copies them to the location from which they will be run -- which is why this step must be performed as root, because this will be some location that ordinary users are not allowed to write.
Of course, if someone else has done the "configure" and "make" steps for you, leaving you to do "make install" -- or its equivalent; installing a pre-compiled binary packages (.rpm or .deb) has essentially the same effect as "make install" -- then the locations of certain files will be prescribed. Some standard is required against which pre-compiled packages can be expected to work. Hence, LSB.
Your distributor has already configured and compiled the source to create .rpms or .debs. They chose somewhere sensible to put the files, *which may not be the same place the package author chose*. In fact, there's a good chance it won't. By convention, under Linux, /usr/ is used by package managers -- and /usr/local/ is left for packages installed outside of any package management system. Files in /usr/ are liable to get stomped on. Almost any package you download in source form will by default install itself somewhere under /usr/local/, because that location is "safe" from interference. If you want it somewhere else, you have to say so.
Distributions typically want their pre-compiled packages to have binaries and libraries in /usr/ and their configuration files in /etc/, so they give appropriate parameters to configure. Even pre-compiled binaries from closed-source packages are often placed in /usr/local/ to protect them from package managers.
The Apache httpd server is a complex piece of software -- so complex that even its configuration system is itself configurable. Debian (for it is they who supply Ubuntu) have (IMHO) improved Apache's configuration system for the 2.0 release, by breaking up the old, monolithic configuration file into logical, "feature-sized" units. It takes some getting used to, if you've grown up with the "old" way, but it definitely makes sense.
Part of the problem is the way we've all got used to a very centralised culture, where local dealers don't modify manufacturers' products anymore. Once upon a time, all cars were shipped from the factory with a very basic specification, and garages would enhance each one to the buyer's preference. A modern-day consumer spirited back to those times would naturally tend to take up any problems with the car manufacturer, not the dealer who supplied it.
Open Source is a very de-centralised model, wherein everyone must take responsibility for their own actions. You shouldn't change anything unless you are prepared to document your changes.