My own observation is that one of the uses
of וַיֹּאמַר rather than וַיּאמֶר is stylistic, namely when an additional
verb is assigned to the subject. Here are some examples:
בראשית יד:יט וַיְבָרְכֵהוּ, וַיֹּאמַר:
בָּרוּךְ אַבְרָם
בראשית יח: כג וַיִּגַּשׁ אַבְרָהָם, וַיֹּאמַר
במדבר
כג:יב וַיַּעַן,
וַיֹּאמַר: הֲלֹא, אֵת אֲשֶׁר יָשִׂים
שופטים כ:ד וַיַּעַן הָאִישׁ הַלֵּוִי, אִישׁ הָאִשָּׁה הַנִּרְצָחָה--וַיֹּאמַר
This style is not followed,
however, when ויאמר is followed by an infinitive,
such as ל... or לו
or אליו, as in:
בראשית כז:לז וַיַּעַן יִצְחָק
וַיּאמֶר לְעֵשָׂו
I
found only one exception to this rule in Chumash, where even though there is
another verb, plus no infinitive after the ויאמר,
the nikud is וַיּאמֶר:
בראשית מ:יח וַיַּ֤עַן
יוֹסֵף֙ וַיֹּ֔אמֶר זֶ֖ה פִּתְרֹנ֑וֹ שְׁלֹ֙שֶׁת֙ הַסַּלִּ֔ים שְׁלֹ֥שֶׁת יָמִ֖ים
הֵֽם:
(In the rest of Tanach,
my Concordance tells me that there are 32 more instances of ויען...ויאמר, but I have not gone through them to see
whether in those cases the ויאמר is always followed by
an infinitive.)
But another use of vayoMAR vs.
vayoMER might warrant correction in instances where וַיֹּאמַר occurs. When ויאמר is
followed by a name, וַיֹּאמַר makes it very
clear, by the pause, that the one named is not the one speaking, but part of
the quote. This happens often when it’s Hashem or
Elokim that is the word following ויאמר:
בראשית יח:ג
וַיֹּאמַר ה' אִם-נָא מָצָאתִי חֵן בְּעֵינֶיךָ
Viz., it should not be
understood as "And Hashem said, "If I have found favor in your
eyes...". It should be read and understood as, "And he said,
"Hashem, if I have found favor in your eyes...".
Another example:
בראשית טז:ח וַיֹּאמַר הָגָר שִׁפְחַת שָׂרַי אֵי-מִזֶּה בָאת
— וַיֹּאמַר
tells you not to read the verse as saying, “And Hagar said, ‘Servant maid of
Sarai, from where are you coming?” but rather, “And he said, “Hagar, servant
maid of Sarai…’ ”
This example also shows that
scripture uses וַיֹּאמַר for this purpose even
when other indicators already make it clear. After all, the masculine ויאמר rather than the
feminine ותאמר already makes it
clear that it is not Hagar speaking.
In the pasuk you write about, וַיִּיקַץ יַעֲקֹב מִשְּׁנָתוֹ וַיֹּאמֶר אָכֵן יֵשׁ ה' במקום הזה, there is apparently no
fear that one would think that "אכן" is the name
of a person, so writing וַיֹּאמַר would be unnecessary.
In conclusion, I stand by my assertion that the correction in this case was clearly unwarranted. However, my assertion that the difference between the two is universally insignificant was also equally faulty.