daijs: 物事の始まりや、問題の起きた理由などに立ち戻って論じること。また、そのような論調。
jitsuyo: 物事を原初に立ち返って論じること、さかのぼって必要性や存在意義などを問うこと、などを意味する表現。「どのようにするか」を議論しているときに「そもそも、どうしてそれが必要か」という問いを蒸し返すようなあり方。

I think that gloss was fine. The "going back" aspect is important.
For x-refs, I recommend always typing the form of the word you want ([see=そもそも] rather than [see=1006950]) so that obscure kanji isn't carried over.
I think the そもそも in this expression comes from the adverbial usage (see the jitsuyo definition).

@@ -12 +12,3 @@
-<xref type="see" seq="1006950">抑・そもそも・3</xref>
+<xref type="see" seq="1006950">そもそも・1</xref>
+<gloss>going back to the beginning (in a discussion, argument, etc.)</gloss>
+<gloss>returning to the fundamental points (of the issue at hand)</gloss>

@@ -13 +13 @@
-<gloss>going back to the beginning (discussion, etc.)</gloss>
+<gloss>discussion of how things began (in the first place)</gloss>

ＫＯＤ追加語彙: その問題を深く理解するためにはそもそも論が必要だ. To really understand the issue, we 
have to go back to the beginning.

@@ -12 +12,2 @@
-<gloss>an expression that discusses things back to the beginning</gloss>
+<xref type="see" seq="1006950">抑・そもそも・3</xref>
+<gloss>going back to the beginning (discussion, etc.)</gloss>