I concur, that's why I like the current limits implied by ST:ENT with Replicator Tech not being able to create living cells and Transporters only being able to "Move Matter" around by Phasing and not necessarilly restoring a previous state of a person or create new living matter.
Limits schmimits...
The ST: ENT automated station had similar... albeit different (and probably inferior) technology vs 24th century UFP.
UFP replication and transporter tech were not suggested to have same limits... in fact, we have seen that in TNG, they were able to reconstitute Picard from his old pattern... revert Pulaski's DNA and restore her youth, and the fact that with a mishap it can easily revert people to a younger age with their memories intact, and modified to return them to their original age (again, with memories intact)... oh and the biofilters that are present in the transporters are there to filter out any unwanted pathogens.
I'd say the UFP would spend about a good amount of time studying and testing this option for the transporters before the modifications are allowed to be used by the population at large (at least, those who want it)... but I suspect that it wouldn't take very long amount of time for this to occur.
If algorithms were used to automate the R&D... then a few hours to days at most... with an extra amount of say 1 year to 'perfect' it.
The UFP replication technology in the 24th century was described to convert energy into matter too... this wouldn't be very surprising when you think about the premise that UFP is comprised of over 150 alien species working and sharing their knowledge, technology and resources openly.
Whereas most others organisations are 'empires' with 1 dominant species that seemingly can develop their own technology etc... but in some respects, woldn't be able to replicate the same 'quality' as UFP would because they don't share the same cooperation mentality or seeing 'smaller alien civilizations' as equals... this is probably going to be reflect in their R&D.
I would imagine that finer control of what to reconstitute from the older pattern would take a bit of finesse, but nothing too problematic (since it was already done).
Also, the transporter wouldn't need to be used for something like that... it would be mainly a last ditch effort to try in case medical technology and science failed and predominantly in cases of body regeneration.
Cancer for example is a non-issue in the 22nd century even... since then, most 'issues' that would threaten people would significatly reduce by the 24th century and wouldn't require a transporter.
The transporter could potentially be used for tissue regeneration... aka, revert the body to an earlier stage of development... not necessarily adolescence, but say late teens or early 20ties if it was wanted... or the age would be optional - but again, this doesn't seem to be used even in the 32nd century so its a moot point.