Among the information that libtool archives a record of the libraries that they describe is the expected installation location. This information is recorded when the library is created. Then you can install it in another place, but libtool will complain. Often the libtool warning is harmless.
To avoid this warning, you must tell libtool the same installation location during build that you do during installation. You present one way to do this in the question, but if you use the standard Autotools build system, it is better to specify the configure installation prefix:
./configure --prefix=/my/path make make install
Alternatively, if you are installing in the staging area, for example, to create an RPM, use DESTDIR during installation. libtool will still warn, but you will avoid spoiling anything else:
./configure make make install DESTDIR=/staging/area
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