TL;DR:
Pattern Editing Mode uses the next layer highlight color in the Layer Highlight color list, as if Pattern Editing were a "layer" and not actually a "mode."
Illustrator CS6 has a bug and the application uses an internal list which is different than the list displayed to users, see below. The bug may also be present in CC versions.
Please bear with me... it takes some explaining of Layer Highlight functionality in case one's not familiar with it. In addition, there are app inconsistencies (i.e. bugs) which may be present depending upon the version of AI is use.
Some of the issues may be resolved in newer versions of Illustrator, I don't know.
For anyone using legacy versions, be warned.... it can be tricky.
Look at the Layer highlight color list by double-clicking a layer thumbnail in the Layers Panel....

The order of these colors matters (*most of the time).
When you add a new Layer the next color down is designated as that new layer's highlight color.
New files start with Layer 1 set to Light Blue
... so if a Layer is added, Layer 2 will be set to Light Red
...

This continues down the list for layers - Layer 3 will have Green
set highlights...

.... Layer 4 Medium Blue
, etc.....
*The "broken" part in some versions of Illustrator...
Some versions of Illustrator don't adhere to the list order at all times.
For example Illustrator CS6 will skip Magenta
and Cyan
, jump straight to Yellow
, then go back to Magenta
, then Cyan
. So for CS6 the app actually uses a variation of what is displayed to the user.
Illustrator CS6's actual list order:
Light Blue
Light Red
Green
Medium Blue
Yellow
Magenta
Cyan
Light Grey
Black
...etc.
I do not know why Yellow comes before Magenta when the app auto-assigns layer highlight colors. It appears to be a bug in CS6 to me. It may or may not be different in any version of AI.
(A user can manually change the layer highlight color by picking a color from the list. If a different highlight color, other than the default, is chosen the list starts over from the user-assigned color. If Layer 3 is set by the user to Light Blue
for the highlight color, the list starts over... Layer 4 will then use Light Red
, Layer 5 Green
, etc. )
The Tricky Part for Pattern Editing Mode
Pattern Editing Mode uses the next color in the list as if it were a "layer" and not a "mode"
What this means is..
For example using Illustrator CS6 (and noting the bug/list above)... if the Layer highlight color is set to Medium Blue
... looking at the (actual) list above, Yellow
will be the next color. So when entering Pattern Editing Mode, Yellow
is used as the highlight color.

This is also seen when a new Layer is added.. the highlight for the next layer is Yellow
:

So...
To change the Pattern Editing Highlight Color, change the highlight color assigned to the top Layer in the Layers Panel. Assign the color before the color you actually want.
If you want the Pattern Editing Highlight to be Green
, assign Light Red
as the highlight color for the top layer in the Layers Panel.
I did warn you it's a tad tricky.
I can't really explain the Adobe logic behind all of this.