I think there are three reasons for different results:Mine is set up as IMAP using the "GMail" default option that one gets one when first selects "add an account." (FWIW, that also doesn't explain why iOS itself gives a different set of search results from the "Spotlight" screen than it does from the Mail app.)
1. I'm pretty sure Spotlight does not search email bodies, only subject/to/from. Tried it just now and that seems to be the case.
2. Spotlight only searches local content. So if you tell Mail to keep 50 emails locally, you only get those 50 when you search via spotlight. It does not perform a server-side search on your email account(s).
3. Spotlight searches all your email accounts/mailboxes/folders/etc, whereas Mail searches are context-specific. (If you are in your inbox when searching only the inbox gets searched, if you are in "All Mail" folder, it searches everything, etc)