Actually any self-identification should have the option of "non-response" or unknown which allows applicants to opt out for whatever reason. If they opt out and there has been no visual identification, they should not be included in any adverse impact analysis that you analyze for your applicants/hires.
Here's what we tell our clients: Provide all applicants the option to self-identify either electronically or by paper. If they opt out electronically, but show up for an in-person interview, provide them another opportunity. If they opt out again, then visually identify but do not make questionable guesses. It is really hard in some cases to identify the race/ethniciy but gender you can at least identify. It is possible you may have only gender, but the ethnicity is unknown for analysis purposes. Finally, anyone that is hired is given the opportunity to identify again and at this point there should be little reason to opt out however, you can't force them to identify so you may be left with the visual.
The visual identification has very little to do with how we "see" people and discrimination but has more to do with having an accurate data set for performing adverse impact analysis and making sure your recruiting efforts are attracting a representitive sample of the population and your hiring decisions are fair and unbiased. Without any kind of visual identification or collection of the data, there is no way to effectively measure this.