That's interesting. Do you still have those files or did you irreversibly delete them? I cannot answer why SFC still detects our CRT if you removed all of its files. I tried to reproduce your issue on Windows 8.1 and 10 x64 but was unable to reproduce the issue. This makes me wonder if you really hadn't those manifest somehow broken.
Can you try to reinstall Avast? It might fix it by reinstalling CRT again.
All of the following were permanently deleted:
C:\Windows\WinSxs\Manifest\*_avast.*
C:\Windows\WinSxs\*_avast.*
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\SideBySide\Winners\*_avast.*
I have now reinstalled Avast 2016.11.2.2262 with my usual component selection:

Next I restore my .avastconfig settings and reboot.
Then I login to my Avast account and always get this error:
Unexpected Error
An unexpected error occurred on the server, we are working on the solution.
Refresh
another reboot usually fixes this issue.
Finally I have run sfc /scannow which results in:
Windows Resource Protection found corrupt files but was unable to fix some
of them. Details are included in the CBS.Log windir\Logs\CBS\CBS.log. For
example C:\Windows\Logs\CBS\CBS.log. Note that logging is currently not
supported in offline servicing scenarios.
Here are the offending lines in the CBS.log:
2016-05-31 14:33:04, Info CSI 00004e9d [SR] Beginning Verify and Repair transaction
2016-05-31 14:33:04, Info CSI 00004e9e Manifest hash for component [l:73 ml:140]"amd64_avast.vc140.crt_fcc99ee6193ebbca_14.0.23918.0_none_53c8344321b452ba" does not match expected value.
Expected:{l:32 b:714cddc73198abfd1a1a7dccbbca0808eda040d50b048b7e421d7afb8e2ac6b8}
Found:{l:32 b:b77d27df43c464ca24067666962175bd050201195a9a3e9f4021c89abb2c29c0}.
2016-05-31 14:33:04, Info CSI 00004e9f Unable to load manifest for component [l:73 ml:140]"amd64_avast.vc140.crt_fcc99ee6193ebbca_14.0.23918.0_none_53c8344321b452ba"
2016-05-31 14:33:04, Info CSI 00004ea0 [SR] Cannot verify component files for Avast.VC140.CRT, version 14.0.23918.0, arch amd64, versionScope neutral, pkt {l:8 b:fcc99ee6193ebbca}, type [l:5]"win32", manifest is damaged (TRUE)
2016-05-31 14:33:04, Info CSI 00004ea1 Manifest hash for component [l:71 ml:140]"x86_avast.vc140.crt_fcc99ee6193ebbca_14.0.23918.0_none_9b756b1a36307bc0" does not match expected value.
Expected:{l:32 b:4379430502b6887d62d4283c0bfcb6aaf7b65e2d559321ca9b05a5c80c3f4357}
Found:{l:32 b:d6b86bd6da85aef647b9c45e336c2ca37eda2e509c81bcf41b9bf06ca7c4f148}.
2016-05-31 14:33:04, Info CSI 00004ea2 Unable to load manifest for component [l:71 ml:140]"x86_avast.vc140.crt_fcc99ee6193ebbca_14.0.23918.0_none_9b756b1a36307bc0"
2016-05-31 14:33:04, Info CSI 00004ea3 [SR] Cannot verify component files for Avast.VC140.CRT, version 14.0.23918.0, arch x86, versionScope neutral, pkt {l:8 b:fcc99ee6193ebbca}, type [l:5]"win32", manifest is damaged (TRUE)
2016-05-31 14:33:04, Info CSI 00004ea4 [SR] Cannot verify component files for policy.11.0.Avast.VC110.CRT, version 11.0.60610.1, arch x86, versionScope neutral, pkt {l:8 b:2036b14a11e83e4a}, type [l:12]"win32-policy", manifest is damaged (FALSE)
2016-05-31 14:33:04, Info CSI 00004ea5 [SR] Repair complete
This fiasco all started with my post Manage Accounts crashes GUI dated 12/04/2016 and the subsequent background fixes and the forced SafeZone browser background install, which has screwed things up for me on all my Windows 10 Pro 64-bit PCs. It does not affect any of my Windows 8.1 64-bit PCs that I administer.