diff --git a/synapse/handlers/register.py b/synapse/handlers/register.py
index cff6b0d375..3c142a4395 100644
--- a/synapse/handlers/register.py
+++ b/synapse/handlers/register.py
@@ -168,6 +168,7 @@ class RegistrationHandler(BaseHandler):
         Raises:
             RegistrationError if there was a problem registering.
         """
+        yield self._check_registration_ratelimit(address)
 
         yield self.auth.check_auth_blocking(threepid=threepid)
         password_hash = None
@@ -414,6 +415,30 @@ class RegistrationHandler(BaseHandler):
             ratelimit=False,
         )
 
+    def _check_registration_ratelimit(self, address):
+        """A simple helper method to check whether the registration rate limit has been hit
+        for a given IP address
+
+        Args:
+            address (str): the IP address used to perform the registration.
+
+        Raises:
+            LimitExceededError: If the rate limit has been exceeded.
+        """
+        time_now = self.clock.time()
+
+        allowed, time_allowed = self.ratelimiter.can_do_action(
+            address,
+            time_now_s=time_now,
+            rate_hz=self.hs.config.rc_registration.per_second,
+            burst_count=self.hs.config.rc_registration.burst_count,
+        )
+
+        if not allowed:
+            raise LimitExceededError(
+                retry_after_ms=int(1000 * (time_allowed - time_now))
+            )
+
     def register_with_store(
         self,
         user_id,
@@ -446,22 +471,6 @@ class RegistrationHandler(BaseHandler):
         Returns:
             Deferred
         """
-        # Don't rate limit for app services
-        if appservice_id is None and address is not None:
-            time_now = self.clock.time()
-
-            allowed, time_allowed = self.ratelimiter.can_do_action(
-                address,
-                time_now_s=time_now,
-                rate_hz=self.hs.config.rc_registration.per_second,
-                burst_count=self.hs.config.rc_registration.burst_count,
-            )
-
-            if not allowed:
-                raise LimitExceededError(
-                    retry_after_ms=int(1000 * (time_allowed - time_now))
-                )
-
         if self.hs.config.worker_app:
             return self._register_client(
                 user_id=user_id,
diff --git a/synapse/storage/data_stores/main/registration.py b/synapse/storage/data_stores/main/registration.py
index f70d41ecab..ee1b2b2bbf 100644
--- a/synapse/storage/data_stores/main/registration.py
+++ b/synapse/storage/data_stores/main/registration.py
@@ -488,14 +488,14 @@ class RegistrationWorkerStore(SQLBaseStore):
         we can. Unfortunately, it's possible some of them are already taken by
         existing users, and there may be gaps in the already taken range. This
         function returns the start of the first allocatable gap. This is to
-        avoid the case of ID 10000000 being pre-allocated, so us wasting the
-        first (and shortest) many generated user IDs.
+        avoid the case of ID 1000 being pre-allocated and starting at 1001 while
+        0-999 are available.
         """
 
         def _find_next_generated_user_id(txn):
-            # We bound between '@1' and '@a' to avoid pulling the entire table
+            # We bound between '@0' and '@a' to avoid pulling the entire table
             # out.
-            txn.execute("SELECT name FROM users WHERE '@1' <= name AND name < '@a'")
+            txn.execute("SELECT name FROM users WHERE '@0' <= name AND name < '@a'")
 
             regex = re.compile(r"^@(\d+):")