A good VPN does not necessarily make the internet noticeably slower. But an extra route can add delay: a response has another part of the journey and additional processing.
An extra leg
Normally: you → site. With a VPN: you → VPN server → site.
Server load
If the selected VPN server is busy, waiting for a response can grow.
Extra processing
A connection may need more steps before data is transferred.
The Flash Route approach
Flash Route does not put the entire browser through a special route. If YouTube is selected, routing applies to YouTube. A regular site keeps the normal connection.