build: Add -isystem and set specialized flags as a last configuration step

This change prevents global flags from interacting with library/feature
detection scripts.

Change-Id: I0423b6ba5b2bfefa90a88aaebba44f15b00043bb
Refs: #4296
diff --git a/wscript b/wscript
index 01139df..9fcb8b3 100644
--- a/wscript
+++ b/wscript
@@ -35,6 +35,8 @@
 
     conf.check_boost(lib=boost_libs, mt=True)
 
+    conf.check_compiler_flags()
+
     conf.load('sanitizers')
 
     # If there happens to be a static library, waf will put the corresponding -L flags