It can be used for that if you want - yes.
I believe that it was designed for situations where you want to just create a consensus transcriptome reference GTF from multiple samples, whatever they may have been. Take a look at the release notes:
1/3/2016 - v1.2.0 release
new feature: a "transcripts merge" usage mode of StringTie which is triggered by the new --merge option; with this option StringTie expects as input a list of GTF files and merges/assembles all these transcripts into a non-redundant set of transcripts. This performs a
function similar to the CuffMerge script in the Cufflinks/Tuxedo suite -- please see the updated protocol in the manual.
an improved "estimation only" usage mode (-e option); in this mode only, StringTie now assigns reads to partially covered reference
transcripts as well, therefore relaxing the previous requirement that reference transcripts need to be covered end-to-end in order to be
found as expressed.
improvements in dealing with abnormally large bundles by filtering of likely spurious spliced alignments produced by some aligners (e.g. STAR); note that HISAT2, used with the --dta option, is now the recommended aligner to use for StringTie.