I get creeper-face, chiseled sandstone, when I use "minecraft:sandstone".

Sandstone filler marker, lava oceans
allBiomes = forAllBiomesExcept(40-58, 163, 164, 166, 167)
## EXCLUDE TF !! **
# Also exclude Mesa Plateau M (normal 166 and FM 167),
# and Savanna M (normal 163 and plateau 164)
### allBiomes.set("topBlock", "ganyssurface:coarse_dirt")
allBiomes.set("fillerBlock", "minecraft:sandstone")
allBiomes.set("liquidFillerBlock","minecraft:lava")

mesaAlters = forBiomes(37, 165)
#37 is normal mesa, to change. 165 is bryce, to change
#38 is Plateau F, 39 is Plateau, both are hellified below.
#166 and 167 are the M plateuas, left unchanged
# These biomes are low enough to have all that red sand.
# They default to sand and hardened clay.
mesaAlters.set("topBlock", "minecraft:sandstone")

Fixing this would require overhauling a portion of the generation code, something I'm not going to do with BiomeTweaker. I'm going to consider it as an unfortunate side effect.

Hope you don't mind, I edited your comment to use formatting for code.

I was unable to reproduce this in a plain installation. It seems like something else you have installed is editing metadata. I recommend you try removing mods until you find the one messing it up. I'd also like a mod list.

And the funny thing: it's biome dependent. It was messing up in mesas.

Mod list?

total 32664
0 1.7.10/
8 1.7.10-AmazingChicken-0.1.0s.jar
68 1.7.10-ExpandedIndustry-0.5.2b.jar
420 1.7.10-HardLibCOG-0.5.2a.jar
776 1.7.10-HarderOres-0.5.2d.jar
252 1.7.10-HarderUnderground-0.5.2d.jar
188 1.7.10-HarderWildlife-0.5.2e.jar
804 AncientTrees-1.7.10-1.3.1.jar
88 AppleCore-mc1.7.10-1.1.0.jar
28 BetterSprinting.jar*
156 BiomeTweaker-1.7.10-0.7.49.jar
24 CaveControl 1.7.10 V6a.jar
1032 CoFHCore-[1.7.10]3.0.2-268.jar.off
268 CoFHLib-[1.7.10]1.0.1-151.jar.off
156 CodeChickenCore-1.7.10-1.0.4.35-universal.jar
400 CustomOreGen-1.7.10-1.2.18.jar.off
1528 DragonAPI 1.7.10 V6f.jar
60 FiniteFluids 1.7.10 Concept Mod.jar.off
504 Ganys End-1.8.8.jar
768 Ganys Nether-1.7.8.jar
924 Ganys Surface-1.10.0.jar.off
324 InGameInfoXML-1.7.10-2.8.1.80-universal.jar
48 KoreSample-1.7.10-1.2.5.jar
60 LegacyCraft 1.7.10 V6a.jar
204 Loot++-0.12.jar
60 LunatriusCore-1.7.10-1.1.2.21-universal.jar
40 MobiusCore-1.2.3_1.7.10.jar
92 MystNEI-Plugin-1.7.10-02.01.00.00.jar
272 NEIPlugins-MC1.7.10-1.1.0.11-unofficial.jar
4 NoVoidFog_1.7.10.zip
500 NotEnoughItems-1.7.10-1.0.4.94-universal.jar
176 OpenEye-0.6-1.7.10.jar
5004 Opis-1.2.3_1.7.10.jar
252 PlayerAPI-1.7.10-1.0.jar*
6436 RotaryCraft 1.7.10 V6f.jar
172 SpACore-1.7.10-01.05.01.00.jar
20 UpdateCheckerMod-1.7.10.jar
48 WAILAPlugins-MC1.7.10-0.0.1-10.jar
536 Waila-1.5.10_1.7.10.jar
28 WailaNBT-1.7.10-1.4.jar
80 Wawla-1.2.1_1.7.10.jar
132 XRay-3.0.1.beta.jar
8 ZoomMod-1.2_1.7.10.jar
8 [1.7.2] ChickenShed (v1.1.3).jar
116 fastcraft-1.21.jar
32 lloverlay-0.23a-10.12.0.1007-forge.jar
2080 mystcraft-1.7.10-0.11.5.00.jar*
56 mystcraft-panels-1.7.10-0.0.0.10.jar*
132 neiaddons-mc1710-1.12.3.11.jar
0 resources/
2348 rftools-2.80.jar.off
128 ttCore-MC1.7.10-0.1.0-67.jar
3504 twilightforest-1.7.10-2.3.5.jar
1312 worldedit-forge-mc1.7.10-6.0-beta-01.jar

Turns out mesa biomes set some blocks metadata to 1 (among other values). That is how they get the colored clay layers. Unfortunately, the code in which this is set is run after any Forge hook, so there's no direct way I can fix this.

I'll keep thinking of ways to fix this, but I can't guarantee anything.

No problem.

I wound up having to leave mesas as sand/clay, and doing some work with COG to make them the way I wanted. It's good enough.