Makefile.autotools.in: fix libtool patching

Fixes two issues with libtool patching:

- It seems like the default value for <package>_LIBTOOL_PATCH only gets
  set AFTER the ifdef check, so the conditional was never taken. Fix it
  by instead checking that it isn't explicitly set to not do the patching
  instead.
- The $i in the libtool patching for loop needed an extra level of escaping
  to work.

Signed-off-by: Peter Korsgaard <jacmet@sunsite.dk>