barker8

Because you've increased the total goals expectation from around 2.41 to 2.61, simple as that. As the calculator seems to be pretty much be using poisson to calculate the odds, it's underestimating the chances of both teams scoring the same number of goals (i.e. the draw).
As has been stated, just using the data you're using will never get you that close to the "true" odds but it's fine if you're just dipping your toe in the waters or are doing it for fun. Even if you used numbers based on 50% of your calculation and 50% of the average home/away goals for the whole league it would probably get you closer to the market odds.

If the significant absence was in the underdog's defence, for example, you could increase the total goals expectation and the supremacy by the same amount, e.g. add 0.2 onto both so that 1.5/1.1 became 1.7/1.1. That would impact match and overs odds.

Your goals and supremacy numbers are probably unrealistic. The spreads imply total goals are expected to be around 2.2 or 2.25 with Boro supremacy 0.4 or 0.45. Maybe those numbers would give you closer to the market odds. If you really trust your numbers, then take the value you've found (but if it was that easy, everyone would be doing it)!

Just to add, you'll never get true numbers just by crunching the averages for each team this season, you'll need to be far more sophisticated than that to beat the bookies but, if you are going to do that, your figures in this case have been badly skewed by the unusually low number of goals Boro have conceded at home. As they're away, you'd arguably be better (but not that much) focusing on respective home/away totals for each team.

Because you are using a simple formula and goals are not the best measure of team quality. They are rare events and subject to chance. Also, a high scoring game can skew a team's average. 
You may want to read about Expected Goals. Here is a good article.