I am not entirely familiar with the interaction between xTerior and xCoba, but it seems that Int is not trained to handle Diff[coordinate[]]. It is trained over dx[manifold]. Hence, a solution (although maybe not the optimal one) is to transform the former into the latter using the rule:
rule = {Diff[\[Alpha][]] -> dx[M4][{1, ch1}],
Diff[\[Theta][]] -> dx[M4][{2, ch1}],
Diff[\[Phi]1[]] -> dx[M4][{3, ch1}],
Diff[\[Phi]2[]] -> dx[M4][{4, ch1}]}
Then
Int[\[Xi][a]][Diff[\[Phi]1[]] /. rule] returns b1
Int[\[Xi][a]][Diff[\[Phi]2[]] /. rule] returns b2
Diff[\[CapitalPhi]T] - Int[\[Xi][a]][\[CapitalPhi]T /. rule] /.
rule // Simplification returns 0
I hope this helps!