I will provide answer for IBM Q. There is a language callled QASM. As you can see from the name of the language, it is similar to assembly language known from classical computer.
The language statements are very simple - they involve an operation (i.e. quantum gate) and affected qubits. For example to apply $X$ gate on qubit no. 0, you have to put in
x q, for CNOT gate with control qubit no. 0 and target qubit 1, the statement is
cnot q, q etc. Also special stataments are used for measurement, setting number of qubits in qubit register and bits in classical register. You can also define subroutines which are called custom gates. This all means that you operates on qubit and gate level although logical ones. It is also possible to write a program in QASM using only basic gates which are $U3$ and CNOT on IBM Q (although $U3$ is still not physical gate).
IBM Q also enables you to program a quantum processor with microwave pulses directly (only processor Armonk offers this capability now) which is really physical level, something like programming classical computer by switching particular transistors.
Concerning the possibility of a something going to be obsolete. There is always such risk in any segment of industry, particularly in IT which evolves rapidly.
As I see it, it think to learn QASM/Qiskit is useful as it allows you to get insight how quantum computers work. Then, it would be easy to switch to another language.