After consulting with upstream (who approved my patch and said they intend to apply it upstream) I have gone ahead with the NMU. Final debdiff is attached.
diff -Nru freedv-1.4/debian/changelog freedv-1.4/debian/changelog --- freedv-1.4/debian/changelog 2019-11-18 03:32:07.000000000 +0000 +++ freedv-1.4/debian/changelog 2020-01-07 10:09:41.000000000 +0000 @@ -1,3 +1,10 @@ +freedv (1.4-1.1) unstable; urgency=medium + + * Non-maintainer upload. + * Put x86 specific code behind ifdefs (Closes: 947828). + + -- Peter Michael Green <plugw...@debian.org> Tue, 07 Jan 2020 10:09:41 +0000 + freedv (1.4-1) unstable; urgency=medium * New upstream release diff -Nru freedv-1.4/debian/patches/put-x86-specific-code-behind-ifdefs freedv-1.4/debian/patches/put-x86-specific-code-behind-ifdefs --- freedv-1.4/debian/patches/put-x86-specific-code-behind-ifdefs 1970-01-01 00:00:00.000000000 +0000 +++ freedv-1.4/debian/patches/put-x86-specific-code-behind-ifdefs 2020-01-07 10:09:35.000000000 +0000 @@ -0,0 +1,27 @@ +Description: Put x86 specific code behind ifdefs. +Author: Peter Michael Green <plugw...@debian.org> + +--- freedv-1.4.orig/src/fdmdv2_main.cpp ++++ freedv-1.4/src/fdmdv2_main.cpp +@@ -4496,6 +4496,8 @@ void MainFrame::CloseSerialPort(void) + // Tests the underlying platform for AVX support. 2020 needs AVX support to run + // in real-time, and old processors do not offer AVX support + // ++#if defined(__x86_64__) || defined(_M_X64) || defined(__i386) || defined(_M_IX86) ++ + void __cpuid(int* cpuinfo, int info) + { + __asm__ __volatile__( +@@ -4538,6 +4540,12 @@ void MainFrame::checkAvxSupport(void) + + isAvxPresent = avxSupported; + } ++#else ++void MainFrame::checkAvxSupport(void) ++{ ++ isAvxPresent = false; ++} ++#endif + + #ifdef __UDP_SUPPORT__ + diff -Nru freedv-1.4/debian/patches/series freedv-1.4/debian/patches/series --- freedv-1.4/debian/patches/series 2019-11-18 03:32:07.000000000 +0000 +++ freedv-1.4/debian/patches/series 2020-01-07 10:09:35.000000000 +0000 @@ -2,3 +2,4 @@ HID-PTT debian-version optional-lpcnetfreedv +put-x86-specific-code-behind-ifdefs