So lets say your ISP connects to the destination ISP in japan. Now lets say a VPN company buys a connection from both ISP and puts a data center in say singapore. In this case a VPN would be faster. If the VPN company could only connect to your ISP in japan they would not be any faster.
You are going to have learn all about how the internet actually works to find a vpn company that has better connections. They seldom document enough to figure this out easily. You can if you work at it though get a good guess as to how many things are connected. The key tool is called looking glass. This is a generic term used for web access ISP give into their network. It lets you issue commands on their routers so you can actually look at the routing tables which will show you the path data takes.......It is not as simple as it sounds though it show BGP AS numbers not lists of routers/cites like tracert. Many of these sites allow tracert and ping also.
You are best off starting with a site like this one. It will show you the IP blocks which companies use and how they are generally interconnected. This is high level stuff but it gives you some direction on what ISP you should be checking for looking glass sites.
The reason I suspect the latency maybe different you may have connected to a different data center in the same city or they ISP has multiple IP blocks and they do not advertise them into other ISP the same. This would mean if you were assigned different IP ranges it may not follow the same path. All depends on how the VPN provider got the IP blocks and what aggrements they have with their ISP partners on how they can advertise them.
Now it maybe simpler to brute force try a bunch of vpn providers and see if you get lucky. Learning how BGP works is actually something a very senior network person does, most network guys that do not work for a huge company likely have never seen it.