Really you're entering the world in which you probably want to develop genetic operators that have meaning in your domain. You mention TSP, and correctly point out that the absolute position within the chromosome doesn't matter. There are other permutation problems where this isn't true. The Quadratic Assignment Problem (QAP) is one example. Like TSP, QAP solutions are represented as permutations of integers, and there are plenty of known recombination operators that work on permutations. But you need different operators for these cases. What works well for TSP won't be very good for QAP, and vice versa.
For reference, a good place to start might be the Cycle Crossover (CX) operator. It's defined on permutations, and basically works by looking for "cycles" -- subsets of the indices where the two parents share the same values. For example, if you have parents
P1=<2 3 7 1 4 6 5 8> P2=<4 1 2 6 8 5 3 7>
there's a cycle at the index set {0, 2, 4, 7}. Both parents contain the same four values at those positions in the string -- 2, 7, 4, and 8. You could create two new offspring by exchanging the values at those positions, yielding
C1=<4 3 2 1 8 6 5 7> C2=<2 1 7 6 4 5 3 8>
This gives me two children, both of whom have the property that they inherited information from their parents related to the absolute position of each value in the string.
That may or may not be exactly what you need for your problem. Maybe you don't have true permutations, or maybe something about that operator doesn't work well with your particular problem. The main point is that you need to build operators with intent. The idea has been called "respectful recombination". Understanding what's important in your representation and devising operators that try to respect that property as they pass down information is the name of the game.