I'm sure somebody has a good rationale for why these crossings are being eliminated
Risk reduction. Every at-grade crossing presents a risk to the city and to the railroad.
When Jungus Jordan was councilman I asked him about the Gambrell street crossing just west of the seminary being eliminated (I used that as a bicycle crossing now and again) and he said the city is trying to get rid of as many at-grade crossings as possible to reduce the risk of people/cars getting hit by trains.
That's also why Dutch Branch Road was never made to cross the tracks between Granbury and Oakmont Trail, according to Jungus.
What can be done about these railroad crossings? It would seem like they could potentially be buried in some places, so the street grid could continue above but that is both very expensive and could see how the RR would object to having a RR line out of commission for 1-2 years as it gets buried. Almost seems like would need to be replaced by another location instead of burying in same place.
They're not getting rid of all of them but they are trying to minimize the number of them. Each one represents an increment of risk. If you get rid of one it doesn't necessarily eliminate the risk but it perhaps reduces it by driving people to cross the tracks at bridges and/or at grade crossings that have enhanced features that make them supposedly safer (such as lights and gates instead of lights alone).