If uninative is not in INHERIT, there will be a lot of warnings like the following when install the ext sdk:
WARNING: The quilt-native:do_configure sig is computed to be 2be53622b8c5b6e8156053bfa5fdd825, but the sig is locked to 1dea2d1ace9b9bea1e9564b9c6709b40 in SIGGEN_LOCKEDSIGS_t-x86-64
The quilt-native:do_compile sig is computed to be 71aeabc1dc38d575e8d4a52e1c8d1f07, but the sig is locked to 29116ced7d8dd7f44435df0bbb1b2f27 in SIGGEN_LOCKEDSIGS_t-x86-64
The quilt-native:do_install sig is computed to be 1a741cd3eff119e3dd1c0f085c1df589, but the sig is locked to 490303612172994c44d6f6245c2b0a7c in SIGGEN_LOCKEDSIGS_t-x86-64
The quilt-native:do_populate_sysroot sig is computed to be 598615a6dee5023311f9860759f73af4, but the sig is locked to 3a422026a617d3a3df48813cb588bc3b in SIGGEN_LOCKEDSIGS_t-x86-64

The bitbake-diffsigs shows that the difference is caused by
BUILD_CXXFLAGS's -D_GLIBCXX_USE_CXX11_ABI=0 which is added by 
uninative.bbclass. This is because INHERIT += "uninative" is in
extracted ext sdk's conf/local.conf.

And when do build in the ext sdk fater extracted:
ERROR: quilt-native-0.64-r0 do_configure: Taskhash mismatch 2be53622b8c5b6e8156053bfa5fdd825 versus 1dea2d1ace9b9bea1e9564b9c6709b40 for /buildarea/lyang1/sdk_ext2/layers/oe-core/meta/recipes-devtools/quilt/quilt-native_0.64.bb.do_configure
ERROR: Taskhash mismatch 2be53622b8c5b6e8156053bfa5fdd825 versus 1dea2d1ace9b9bea1e9564b9c6709b40 for /buildarea/lyang1/sdk_ext2/layers/oe-core/meta/recipes-devtools/quilt/quilt-native_0.64.bb.do_configure

If we patch meta/classes/populate_sdk_ext.bbclass to remove uninative:

diff --git a/meta/classes/populate_sdk_ext.bbclass b/meta/classes/populate_sdk_ext.bbclass
index 0f0525d..af2680d 100644
--- a/meta/classes/populate_sdk_ext.bbclass
+++ b/meta/classes/populate_sdk_ext.bbclass
@@ -284,8 +284,11 @@ python copy_buildsystem () {
 
             f.write('DL_DIR = "${TOPDIR}/downloads"\n')
 
-            f.write('INHERIT += "%s"\n' % 'uninative')
-            f.write('UNINATIVE_CHECKSUM[%s] = "%s"\n\n' % (d.getVar('BUILD_ARCH', True), uninative_checksum))
+            # Don't inherit uninative if the build isn't using it
+            if bb.data.inherits_class('uninative', d):
+                f.write('INHERIT += "%s"\n' % 'uninative')
+                f.write('UNINATIVE_CHECKSUM[%s] = "%s"\n\n' % (d.getVar('BUILD_ARCH', True), uninative_checksum))
+
             f.write('CONF_VERSION = "%s"\n\n' % d.getVar('CONF_VERSION', False))
 
             # Some classes are not suitable for SDK, remove them from INHERIT

This still can't fix the problem, there would be strange errors during install ext sdk:

NOTE: Executing RunQueue Tasks
ERROR: Task quilt-native.do_fetch attempted to execute unexpectedly
ERROR: Task quilt-native.do_unpack attempted to execute unexpectedly
ERROR: Task quilt-native.do_patch attempted to execute unexpectedly
ERROR: Task quilt-native.do_configure attempted to execute unexpectedly
ERROR: Task quilt-native.do_compile attempted to execute unexpectedly
ERROR: Task quilt-native.do_install attempted to execute unexpectedly

This is because nativesdk tools can't run:

$ ls ./sysroots/x86_64-wrlinuxsdk-linux/usr/bin/file.real
./sysroots/x86_64-wrlinuxsdk-linux/usr/bin/file.real

$ ./sysroots/x86_64-wrlinuxsdk-linux/usr/bin/file.real
bash: ./sysroots/x86_64-wrlinuxsdk-linux/usr/bin/file.real: No such file or directory

I think that we need add checking in meta/classes/populate_sdk_ext.bbclass to check whether uninative.bbclass is inherited, and error out if not.