That seems a bit ridiculous, lowering suspension can always be aligned properly whether it be to factory specs or not.
Anyhow if that is the story they are telling you, yes you can raise up Tein coil overs quite a bit. You won't be able to bring it up to "stock" height because they are lowered right from Tein.
I wouldn't be switching over to stock suspension until you get another shop to give you a second opinion. I have always ran lowering coilovers on all my JDM vehicles, and had no issues with them being lined up.
Why are they saying they have to be lined up to factory spec? Is it illegal to have lowered cars in your province?
Worse case if you do need to buy factory JDM struts/springs let me know I can source those for you.
Hope I was able to answers your questions.
2001 CDM ITR #01-1324
2018 Civic SI FC3