Never seen the issues you're dealing with on the germination part but as a part time pollen chucker this may help.
IDK how other breeders do this but I can show you what I do.
This pic is the seed harvest from my Haunted Banana F1. After getting the husks off it's a real mixed bag of colors.
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This is where a pheno hunt begins for me.
There's both light and dark tiger stripes, some with only 1-2 stripes, some brown with no stripes, and white all from the same mother and sometimes the same flower.
Color likely depends on how early the pistil was pollinated and genetics crossing or not crossing over.
From here I do a test germination of 15 seeds of each type/color except for the whites. The whites are underdeveloped and honestly, sad to look at and nobody wants those so I try to sift them out.
The dark and lighter striped seeds usually pop at 100%. These are what I send out and prefer to work with but if I send out say 100 seeds there will be everything but white in there.
The lighter brown seeds without stripes are at around a 80-90% germ rate. This was an issue with many of Bodhi's strains as they were always on the light side, no stripes, and germ rates around 80-90%. I believe he was a chronic early chopper
When I take this to F2 I'll drop a split of tigers and no tigers looking for phenos between the two. Generally, tiger stripes lean toward indica and no stripes lean toward hybrid and sativa but there's no guarantee there. However, the more stable the cross develops, the more consistency there will be in harvested seeds and depending on the chosen phenos will produce either all tigers or all brown without stripes