Good observations with the height of the stigma. It is likely you may be selfing some of the flowers when you pollinate. However, this should not have a dramatic influence on the ratios in the F2.
I assume you are talking about intermating the F1 and not making the parental crosses. If you are making the Parental cross, then the potential selfing would have a greater impact.
In the development of the F1 Non-Purple X Purple stem, we have built in a check to be sure you are producing a clean F1 generation and an F2 that will illustrate the ratios. When the cross is made at the parental generation,the pollen is transferred from the purple stem plants to the non-purple stem (recessive) plants and the seed is harvested off the non-purple plants.
In the F1 generation, if you see and seedlings that do not exhibit purple pigment, then you know the non-purple plants were accidentally crossed with other non-purple plants (or selfed) in the parental generation. There is some possibility this can happen, though it is not the typical case. If one checks all plants and removes any of the Non-Purple plants prior to pollinating the F1 generation, then all the remaining plants will be heterozygous for purple and non-puple and the F2 should show a 3:1 ratio. Also remember that the purple expression is affected by light, so be sure your seedlings are close to the lights and receiving adequate intensity to maximize the expression of purple. If you're using fluorescent tubes in a lightbank, it's helpful to check the age of the bulbs and replace them every 3 years at least as their intensity drops off with age.
Also with regard to the lighting, once the plant reaches ~10-12 days old from seeding, the light requirements are less. The plant is shifting from the developmental stage to reproductive stages and we generally raise the lights at this time toanticipate the bolting to flower. For us, raising the lights 4-5 inches above the plants is not unusual at this stage, particularly if we are not going to be around for a couple days.
We do have dwarf parental stocks for the anl/ANL traits. However, no F1 is currently available.
Please let me know if you have any further questions.