Thank you for your feedback.
1) Downloaded latest master (commit ID: ad067c510bacea51755711c1b624da78b1812fba) and commit just before 202503 snapshot (commit ID: 29d9785c2d5f71db7c6ae2834003cd211bd6a421)
2) Compiled both as make CC=clang CXX=clang -f Makefile.dist on my home FreeBSD router (14.2)
3) Checked with Fuji GFX100 test files from rawdb.dnglab.org: four compressed files and two uncompressed via

time ./bin/uncompressed_raw /path/to/*.RAF  

(to check decode time only)

Results
202403 snapshot (+all patches):

real    0m49,581s
user    0m47,898s
sys     0m1,284s

202503 snapshot + two newer changes (PhaseOne checks + CVE numbers):

real    0m44,326s
user    0m42,512s
sys     0m1,468s

The new one looks slightly faster (that could be test variation).

So, please check you're using same compile/etc/ mode for both versions (e.g. same OpenMP support: Fuji decoder is OpenMP-capable).

Regarding your 2nd complain:
It is useless to discuss colors/tint/etc without reference to specific RAW file/processing options used.
The result I see from same files set via dcraw_emu -w -T looks absolutely normal: https://www.dropbox.com/scl/fi/46fz50mtg77ddzytccbpa/Fujifilm-GFX100S-14...