Leverkusen really can't do anything when facing Bayer Munich this season and it's not only proven in the Bundesliga, but it's also been proven through the UCL competition this season where Leverkusen always loses when facing Munich this season. So what you said could be a reality for Munich this season if Munich continues to consistently find points in every remaining Bundesliga match this season.
Xabi Alonso did not leave Bayer Leverkusen last season but I believe he imagined of difficulty and massive challenge in this season. It eventually became true when Bayer Leverkusen failed in Champions League and can not defend their title in Bundesliga. Xabi Alonso already made history with Bayer Leverkusen and what's happening in this season won't change that. He will be remembered by many Leverkusen fans and already marked in this club history.
Untill last season, dominance in the Bundesliga was usually associated with Bayern Munich but then in recent time they are gradually getting back their form and now they have got good rivals making it look like there's a gradual transition from the regular and if Bayern Munich continues slack they may suffer another season of loosing their Bundesliga dominance.
The last season is beautiful for Leverkusen and painful for Bayern Munich by spending a lot of money to purchase Harry Kane from Tottenham Hotspur but failed to win Bundesliga title. They are back with domination in this season but Leverkusen still shown their quality by playing better than other clubs in Bundesliga. They are only weaker than Bayern Munich in this season, and by maintaining better performances than other clubs, it's still a legacy from Xabi Alonso for Bayer Leverkusen.
Could be, could not be. I think Alonso was contemplating two things:
1) His public image and reputation. Having one success with a club and then instantly using it as a steppingstone to leave Bayer behind and join a big club like Bayern or Real Madrid is great for him personally, but it leaves a bad impression behind because he wants to present himself as someone who is loyal and is a builder, a club builder.
2) Relates to 1) as I think he on the one hand he knew the season could not be repeated the same way, but he also knew that something great was growing which he was responsible for. If he were to repeat a huge success in terms of titles, it would make him an even bigger hero forever. Additionally, playing a great CL season with Bayer is far more exciting and amazing than playing a great CL season with Madrid or Bayern. He was dreaming that Bayer may take the CL by storm to some degree and why not, Leverkusen is a strong team able to surprise others, and now they have declined somewhat.