I cannot talk about the efficacy of transferring up using PKSM, however you can see the following details to judge for yourself:
The hex data remains unchanged, so you gonna need to read the data and compare to Gen 5 offsets.
For simplicity, use PKHeX to view the data. If viewing from PKSM, well, I've heard instances that transfers aren't shown correctly.
AFAIK HOME does not modify Met Location. If you use the HOME mobile app, you can even see the actual old met location. (HOME specifically built a function around it, to reference old met locations, cause the data in the met location portion of the pkx format remain unchanged since Gen 5)
In this example, this is a Spinda transferred up from Gen 3. The First Met says Poké Shifter, the transliterated Japanese name of Poké Transfer
FYI, this tidbit can be seen on Poke Transporter's page on bulbapedia
and HOME's page on bulbapedia
However, I understand how it can be missed, as those pages are filled with many many words.
Those pages would cover other modifications as well. Also, PKHeX covers conversion fine, so you could convert up your pk3 to pk6 with no issues.