After sleeping on it and rereading the Meikyo entry, I think this can go ahead. I've discussed the issue in the past with Japanese people, and a common view is that "these days they are called あてじ", which is pretty much in line with that second sense.
How to label thing in entries is another matter. I have trouble with the idea that 啄木鳥/けら can be called "ateji".

There are two issues: (a) the meaning of 当て字 [narrow vs. broad], and (b) the tagging of entries with ateji/gikun/etc.
I'd like to have it discussed more widely, so I'll raise it on the mailing list.

daij

sorted by hits

@@ -8,1 +8,1 @@
-<keb>宛て字</keb>
+<keb>あて字</keb>
@@ -14,1 +14,1 @@
-<keb>当字</keb>
+<keb>宛て字</keb>
@@ -17,1 +17,2 @@
-<keb>あて字</keb>
+<keb>当字</keb>
+<ke_inf>&io;</ke_inf>

meikyo:
あて‐じ【当て字（宛字）】
名
1) 和語・外来語の書き表し方で、漢字本来の意味には関係なく、その音訓を借りてその語の表記に当てた漢字。借字。和語の「甘み」「めでたい」「やたら」をそれぞれ「甘味」「目出度い」「矢」と、外来語の「アジア」「クラブ」「カッパ」「コーヒー」をそれぞれ「亜細亜」「俱楽部」「合羽」「珈琲」と書くなど。
2) 和語・外来語で、漢字の音訓には関係なく、意味が似ていることなどから、ある語を二字以上の漢字を使って漢熟語の形（あるいは、それに準ずる形）で書き表したもの。和語の「のり」「いなか」「きのう」をそれぞれ「海苔」「田舎」「昨日」と、外来語の「ビール」「キセル」「マッチ」をそれぞれ「麦酒」「煙管」「燐寸」と書くなど。
主に、漢語からなる文字列の意味をくみとって、まとめて訓にして読むのが熟字訓。
もともっぱら「宛」を使ったが、今は「当」が一般的。
=====
shinmeikai and gg5 also add:
でたらめな用字。
arbitrarily used substitute character.
=====
wikipedia:
1) 漢字の字義を無視し、読み方のみを考慮して漢字を当てる場合。狭義にはこれのみを指す。仮借を参照。
2) 漢字の読み方を無視し、字義のみを考慮して漢字を当てる場合。広義にはこれを含む解釈もある。なお六書の「転注」がこれを指すと考える学説がある。日本語の熟字訓も含まれる。
wikipedia also supports the 'arbitrary substitute character' sense, but suggests that the reading of the arbitrary character should be the same, which makes it rather redundant with sense 1, AFAICT.

currently our definition for applying the [ateji] tag only includes the strict sense 1) of meikyo.  i think adding the broader sense 2) allows us to greatly expand our definition.  previously we were calling the associated readings [gikun] which sometimes made a mess.
=
sense 2 could probably be worded more clearly

@@ -28,0 +28,4 @@
+<sense>
+<pos>&n;</pos>
+<gloss>kanji used for their meaning, irrespective of reading</gloss>
+</sense>