Yes, you are correct.
However since there is only so much capacity to do genomic tests on PCR swabs in the first place, the proportion of positive tests that are evaluated in this way already drops to a much lower fraction at times when the number of people testing positive becomes very large.
The other way they have been able to monitor for a particular new variant becoming dominant is to check PCR samples for S gene dropout, but since we'e already reached the point where Omicron is shown to be totally dominant using this method, such results are less important right now.
So you are correct to mention this issue, but the implications are of more concern if we are talking about the longer term, eg if they permanently change the PCR testing regime at some future point beyond the current Omicron wave.
