Really bizarre they didn't simply just port Virtua Fighter 5 as a standalone title. Maybe staff at SEGA has no confidence that Virtua Fighter is a strong enough brand to hold on it's own and is using one of their flagship franchises as an excuse to push the game? Which is an uncanny view on things since Virtua Fighter for a long time was one of SEGA's key franchises.
I think it's more like free advertisment for the brand. VF5 is a decade old now, it's had multiple home releases and arcade versions. It had earned its money and many of the people who wanted it already have it. I think now, giving it free in a full price game is a better insentive for people to buy Yakuza and cross promote both series than releasing it alone.
It's almost like a disk with multiple games, people who want Yakuza will buy it for Yakuza, people who want VF5 on PS4 will buy it for VF5 and the only real sacrifice they have made are the niche market that would have baught both seporately at full price.
Plus the gaming landscape has changed in the decade since VF5s release. South East Asia has opened up as a potential massive market for SEGA. Yakuza titles are popular in S.E Aisa now, while I think VF probably hasn't earned that popularity yet.
If SEGA plans to eventually release VF6, putting VF5 in Yakuza 6 is free marketing.