In caret, you can feed original function arguments into caret::train
thanks to the ellipsis ...
mechanism.
For example this code will fit a regularized regression on non standardized data
require(caret)
require(mlbench)
data(BostonHousing)
enet <- train(medv ~ .,
data = BostonHousing,
method = "glmnet",
standardize = FALSE)