diff --git a/tools/build_api.py b/tools/build_api.py
index 4a3de865d3..c647c4ebf6 100644
--- a/tools/build_api.py
+++ b/tools/build_api.py
@@ -411,7 +411,6 @@ def merge_region_list(region_list, destination, notify, padding=b'\xFF'):
     """
     merged = IntelHex()
     _, format = splitext(destination)
-
     notify.info("Merging Regions")
 
     for region in region_list:
@@ -426,20 +425,21 @@ def merge_region_list(region_list, destination, notify, padding=b'\xFF'):
             notify.info("  Filling region %s with %s" % (region.name, region.filename))
             part = intelhex_offset(region.filename, offset=region.start)
             part.start_addr = None
-            part_size = (part.maxaddr() - part.minaddr()) + 1
+            if len(part.segments()) == 1:
+                part_size = (part.maxaddr() - part.minaddr()) + 1
+            else:
+                # make same assumption as in region builder; first segments must fit.
+                part_size = part.segments()[0][1] - part.segments()[0][0]
+
             if part_size > region.size:
                 raise ToolException("Contents of region %s does not fit"
                                     % region.name)
             merged.merge(part)
             pad_size = region.size - part_size
-            if pad_size > 0 and region != region_list[-1]:
+            if pad_size > 0 and region != region_list[-1] and format != ".hex":
                 notify.info("  Padding region %s with 0x%x bytes" %
                             (region.name, pad_size))
-                if format is ".hex":
-                    """The offset will be in the hex file generated when we're done,
-                    so we can skip padding here"""
-                else:
-                    merged.puts(merged.maxaddr() + 1, padding * pad_size)
+                merged.puts(merged.maxaddr() + 1, padding * pad_size)
 
     if not exists(dirname(destination)):
         makedirs(dirname(destination))
diff --git a/tools/config/__init__.py b/tools/config/__init__.py
index e963fd1b38..0e040faf58 100644
--- a/tools/config/__init__.py
+++ b/tools/config/__init__.py
@@ -692,12 +692,13 @@ class Config(object):
         newstart = rom_start + integer(new_offset, 0)
         if newstart < start:
             raise ConfigException(
-                "Can not place % region inside previous region" % region_name)
+                "Can not place %r region inside previous region" % region_name)
         return newstart
 
     def _generate_bootloader_build(self, rom_start, rom_size):
         start = rom_start
         rom_end = rom_start + rom_size
+        max_app_addr = -1
         if self.target.bootloader_img:
             if isabs(self.target.bootloader_img):
                 filename = self.target.bootloader_img
@@ -710,8 +711,23 @@ class Config(object):
             if part.minaddr() != rom_start:
                 raise ConfigException("bootloader executable does not "
                                       "start at 0x%x" % rom_start)
-            part_size = (part.maxaddr() - part.minaddr()) + 1
-            part_size = Config._align_ceiling(rom_start + part_size, self.sectors) - rom_start
+            if len(part.segments()) == 1:
+                part_size = (part.maxaddr() - part.minaddr()) + 1
+                part_size = Config._align_ceiling(rom_start + part_size, self.sectors) - rom_start
+            else:
+                # assume first segment is at start
+                # second at the end or outside ROM
+                # rest outside regular ROM
+                if part.segments()[0][0] != 0x0:
+                    raise ConfigException("bootloader segments not in order")
+                part_size = part.segments()[0][1] - part.segments()[0][0]
+                part_size = Config._align_ceiling(rom_start + part_size, self.sectors) - rom_start
+                if part.segments()[1][0] < rom_end and self.target.restrict_size is None:
+                    if self.target.app_offset:
+                        self.target.restrict_size = "0x%x" % (part.segments()[1][0] - int(self.target.app_offset, 0))
+                    else:
+                        max_app_addr = part.segments()[1][0]
+
             yield Region("bootloader", rom_start, part_size, False,
                          filename)
             start = rom_start + part_size
@@ -722,9 +738,17 @@ class Config(object):
                 start, region = self._make_header_region(
                     start, self.target.header_format)
                 yield region._replace(filename=self.target.header_format)
+
+            if max_app_addr != -1 and self.target.restrict_size is None and not self.target.app_offset:
+                self.target.restrict_size = "0x%x" % (max_app_addr - start)
+
         if self.target.restrict_size is not None:
             new_size = int(self.target.restrict_size, 0)
             new_size = Config._align_floor(start + new_size, self.sectors) - start
+
+            if self.target.app_offset:
+                start = self._assign_new_offset(rom_start, start, self.target.app_offset, "application")
+
             yield Region("application", start, new_size, True, None)
             start += new_size
             if self.target.header_format and not self.target.bootloader_img:
@@ -734,9 +758,7 @@ class Config(object):
                 start, region = self._make_header_region(
                     start, self.target.header_format)
                 yield region
-            if self.target.app_offset:
-                start = self._assign_new_offset(
-                    rom_start, start, self.target.app_offset, "application")
+
             yield Region("post_application", start, rom_end - start,
                          False, None)
         else:
@@ -745,7 +767,7 @@ class Config(object):
                     rom_start, start, self.target.app_offset, "application")
             yield Region("application", start, rom_end - start,
                          True, None)
-        if start > rom_start + rom_size:
+        if start > rom_end:
             raise ConfigException("Not enough memory on device to fit all "
                                   "application regions")