Used "FixedStep" + StartingStepSize for a fixed time step and whichever method for the spatial grid. Ignore the error/warning message about StartingStepSize. You've already complained about error messages, and I have no defense for this one. (It seems StartingStepSize may be used for both temporal and spatial discretization, and it's okay for one but not the other in the examples below.)
Example 1:
\[Nu] = 0.01;
mysol = First[
NDSolve[{D[u[x, t], t] == \[Nu] D[u[x, t], x, x] -
u[x, t] D[u[x, t], x], u[x, 0] == E^-x^2, u[-5, t] == u[5, t]}
, u, {x, -5, 5}, {t, 0, 4}
, Method -> {"MethodOfLines",
"SpatialDiscretization" -> {"TensorProductGrid",
"MinPoints" -> 257, "MaxPoints" -> 257,
"DifferenceOrder" -> 4},
Method -> {"FixedStep", Method -> "ExplicitRungeKutta"}},
StartingStepSize -> 1/2^13]]
Example 2:
mygrid = Join[-5. + 10 Range[0, 48]/80, 1. + Range[1, 4 70]/70];
\[Nu] = 0.01;
mysol = First[
NDSolve[{D[u[x, t], t] == \[Nu] D[u[x, t], x, x] -
u[x, t] D[u[x, t], x], u[x, 0] == E^-x^2, u[-5, t] == u[5, t]}
, u, {x, -5, 5}, {t, 0, 4}
, Method -> {"MethodOfLines",
"SpatialDiscretization" -> {"TensorProductGrid",
"Coordinates" -> {mygrid}},
Method -> {"FixedStep", Method -> "ExplicitRungeKutta"}},
StartingStepSize -> 1/2^13]]
The following gives the distinct step sizes:
u["Coordinates"] /. mysol // Map@Differences // Map@DeleteDuplicates
Examples adapted from the [Method of Lines tutorial.]