When I train my voice and ascending scales I sometimes notice that closed vowels like EE or OO tend to need some modification a few semitones lower than say open vowels like OH and AH. Is this common with the voice?
If I understand your question correctly, you're saying that, if you need to sing a G on a closed-vowel "ee" or "oo," you actually imagine you're singing a different pitch a few semitones away?
This is certainly not normal, and it actually sounds like there are some vocal mechanic problems unrelated to the vowel. Trying singing a given pitch on an open-vowel "oh" or "ah" and slowly change your oral shape to a closed-vowel "ee" or "oo" without changing pitch. This should provide sufficient training to fix this "transposition on the fly" issue you mention.
All vowels really are is spectral content... what you really want is for your formant to be as resonant as possible. Listen for the very highest frequencies to pop out. A lot of budding singers find it more challenging to create the necessary resonance on certain vowels, especially like [i] where the tongue is very high in the mouth, or [u] where the lips are almost closed. Nevertheless, the issue of resonance has to do with undue tension in the tongue and jaw. You need to figure out how to shape your tongue and mouth into the necessary space without any tension at all. It is recommended that you sing a vowel sequence like [a] [o] [i] [o] [e] on some easy scales until you find the same freedom on vowels like [u] and [i] as you already have on [a] and [o]. Good indication that you are making progress is all the vowels will have the same bright, resonant quality, and the rate of vibrato will be constant through vowel changes.