a big difference between the source and target

[kingcrimsonster]

your content is MPEG-2 and thus should be BT.709 and this is what Hybrid assumes since no colorMatrix is specified

When I manual set is to bt601 - avisinth preview working correctly - result preview in right window corresponds to the final encoded file. In this case put the pipette on the green area in right window and measure RGB - 0, 193. 0.
Your quotes

MPEG2 default is BT.709

Hybrid will change the ColorMatrix depending on resolution when 'Adjust by resolution' is enabled.
greater 720*576 -> Rec.709
less or equal 720*576 -> Rec.601

One of these statements must be incorrect.
I'am open in the Hybrid MPEG2 NTSC file with resolution 720-480 - "Colormatrix" set it automatically "From BT601" - this is wrong?

Please, Selur, you yourself make tests of various files 720-480, 720-576 and make sure that the avisinth preview does not differ from the final encoded file.

greater 720*576 -> Rec.709
less or equal 720*576 -> Rec.601

In this case avisinth preview does not differ from the final encoded file.