In this line:
単車は、お世辞にも小綺麗だとは言えない二階建てのアパートの前に停まる。
The lone motorcycle, which couldn't be called 'neat' even as flattery, pulled up to a two-story apartment complex and stopped there.
The clause お世辞にも小綺麗だとは言えない is modifying 二階建てのアパート, not 単車.
So a correct translation would be something like:
The lone motorcycle pulled up and stopped in front of a two-story apartment complex that couldn't be called 'neat' even as flattery.
(Edit: adjusted wording of suggested re-write for better flow)
In this line:
The clause お世辞にも小綺麗だとは言えない is modifying 二階建てのアパート, not 単車.
So a correct translation would be something like:
(Edit: adjusted wording of suggested re-write for better flow)