While you are not tied to one particular book store, not all book stores are compatible.
The real issue is that different vendors use different DRM (copy protection) schemes, and unfortunately, the scheme used by Apple is not at all compatible with Kobo, or any other, non Apple, reader.
There MIGHT be tools available to remove the DRM from Apple but I am not sure (and also, MobileRead does not permit a great deal of discussion on DRM removal).
The other caveat is that there are different formats of eBooks; the main formats are ePub and MOBI / KF8 / AZW; the latter set are used by Kindle's. Yes tools DO exist to convert between formats, but again, they all assume no DRM on the books.
All I can say for DRM removal from ePubs and Kindle formats is to Google for "Apprentice Alf".
Format conversion is best done via a tool called
calibre (see the
calibre forums here for more info).