Indeed, but now that そうこん is tagged as [form], they're best kept separate.

爪痕	61001	32.5%
爪あと	44737	23.8%
爪跡	18883	10.0%
つめ跡	9892	5.3%
ツメ跡	2076	1.1%
ツメアト	737	0.4%
つめあと	5906	3.1%

Merging the two would not be so complicated now that we've adopted a simplified reading restrictions system.

@@ -14,0 +15 @@
+<ke_inf>&sK;</ke_inf>
@@ -17,0 +19 @@
+<ke_inf>&sK;</ke_inf>
@@ -21,8 +22,0 @@
-<re_restr>爪痕</re_restr>
-<re_restr>爪あと</re_restr>
-<re_restr>爪跡</re_restr>
-<re_restr>つめ跡</re_restr>
-</r_ele>
-<r_ele>
-<reb>ツメあと</reb>
-<re_restr>ツメ跡</re_restr>
@@ -32,2 +25,0 @@
-<xref type="see" seq="2846304">爪痕・そうこん</xref>
-<xref type="see" seq="2846304">爪痕・そうこん</xref>

三省堂国語辞典
つめあと「爪痕」... (definitions agree with current definitions, this is the only kanji given, no entry for そうこん whatsoever)

「爪痕(つめあと)を残す」 (a whole NHK article just on this expression, no alt kanji, no alt readings)
https://www.nhk.or.jp/bunken/research/kotoba/20210101_3.html

I see on 2846304 a comment by Jim Breen that there was an abandoned attempt to merge these two entries. (そうこん 爪痕).  I don't have a strong opinion on merging them or not, but this seems to have left an odd situation.

1. The most common reading of 爪痕 appears to actually be つめあと. But if you look up 爪痕 by kanji in this dictionary, you now get an entry with only one reading そうこん, and a reference to this entry, where 爪痕 is a *secondary* reading of つめあと.

2. 爪痕 appears to be the most common kanji for つめあと, not 爪跡.  My modern dictionary, for example, *only* gives 爪痕, and does not even contain an entry for the reading "そうこん".

Beyond my one dictionary reference, you need only google 爪痕 to see that つめあと is the most common reading.  The n-grams already cited here support this interpretation (granted a confounding factor from そうこん). 

I'm submitting a parallel change to the other entry that I think reconciles things "well enough" without merging the two entries.  Mark そうこん as [form], reference this entry using the same kanji 爪痕, re-order the kanji in this entry so that 爪痕 is the most common entry. Provide a back reference from this entry to the other to identify the existence of the literary form.

@@ -4,3 +3,0 @@
-<k_ele>
-<keb>爪跡</keb>
-</k_ele>
@@ -11,0 +9,3 @@
+</k_ele>
+<k_ele>
+<keb>爪跡</keb>
@@ -21 +20,0 @@
-<re_restr>爪跡</re_restr>
@@ -23,0 +23 @@
+<re_restr>爪跡</re_restr>
@@ -31,0 +32 @@
+<xref type="see" seq="2846304">爪痕・そうこん</xref>

daij, prog
G n-grams:
爪痕	61001
爪跡	18883
爪あと	44737
つめ跡	9892
ツメ跡	2076
つめ痕	431
ツメ痕	195

@@ -9,0 +10,9 @@
+<k_ele>
+<keb>爪あと</keb>
+</k_ele>
+<k_ele>
+<keb>つめ跡</keb>
+</k_ele>
+<k_ele>
+<keb>ツメ跡</keb>
+</k_ele>
@@ -11,0 +21,8 @@
+<re_restr>爪跡</re_restr>
+<re_restr>爪痕</re_restr>
+<re_restr>爪あと</re_restr>
+<re_restr>つめ跡</re_restr>
+</r_ele>
+<r_ele>
+<reb>ツメあと</reb>
+<re_restr>ツメ跡</re_restr>
@@ -20 +37,2 @@
-<gloss>scar</gloss>
+<gloss>scars (e.g. of war)</gloss>
+<gloss>traces (of damage)</gloss>