It shows what it can show, based on the available modern data, with all the sampling bias, migrations and changes which happened in the last thousands of years. Therefore its valuable, but it doesn't tell us where a haplogroup started. Even the diversity view can be misleading, because even "diversity can migrate" and sampling bias affects it too. If e.g. in an area of Western Ukraine lived a Daco-Thracian tribe which was 80 % E-V13, but this migrated away and its remnants being almost completely annihilated by later migrations, it won't show up. And if they cremated, we also have a problem with their ancient DNA track record. Only dense sampling all around throughout the ages can help and testing way more moderns from all relevant countries.
Phylogeographer has an additional big disadvantage of being based on YFull only. On YFull are more Albanians tested than on FTDNA, but nearly all other people have more people tested on FTDNA, and their data is completely missing. E.g. some months ago (don't know if it changed), there was probably just one Moldovan E-V13 tested, just ONE! On FTDNA its not a lot as well, but at least there are 3, which is still a joke considering the total percentage of E-V13 in Moldova. For Romanians its 10 vs. 20, of which a lot are no ethnic Romanians, but still double the time people tested on FTDNA BigY in comparison to YFull.
The most extreme its for Bulgaria, because it has 60 people, mostly ethnic Bulgarians, on FTDNA tested, yet on YFull are just 11! So almost 6 times the size of FTDNA sample, with Bulgarians being in many important branches and well-represented. You find them on YFull as well, but much fewer of them. That's all data which phylogeographer doesn't take into account.
The FTDNA data being better represented on its new Discovery tool site and on scaledinnovation:
http://scaledinnovation.com/gg/snpTracker.html
But if tracking down various subclades with scaledinnovation, they constantly being pulled too far to the West. This would change with more data from countries like Slovakia, Romania, Moldova, Ukraine etc.