由同事回答（感谢Michael Schwartz）。简单的向量化解决方案是创建用于重组字节向量值的索引的向量。我有两个可行的解决方案：

# Test on a vector with 24 bytes, convert to 6 doubles of 4 bytes each
values <- c(1, 12, 123, 1234, 12345, 123456)
pc_bytes0 <- writeBin(values, raw(), size = 4)

# Need to shuffle the byte order to reproduce DEC order
# using same procedure we will use to unshuffle

# Swapping needed to convert from PC to DEC byte order
# DEC byte 1 -> 3, 2 -> 4, 3 >- 1, 4 -> 2
byte_adjust <- rep(c(2, 2, -2, -2), 6) 
# Original index order
pc_byte_index <- seq(1:24) # original byte order
# New index order for DEC data storage, add adjustment vector
dec_byte_index <- pc_byte_index + byte_adjust
# Now reshuffle the original data using the index to get the DEC order
dec_bytes <- pc_data[dec_byte_index]
# This what readBin(raw()) will return from DEC file, 
# so actual process starts here.
# Note: To get the true DEC byte array we would have to subtract 01 
# from the 2nd byte in each 4 byte sequence

# Approach 1, make a long vector of original byte order and another of offsets
# and add together
# Data is in DEC sequence, so make vector of original order
dec_byte_index <- seq(1:24) # original byte index order
# These are the index offsets needed
byte_adjust <- rep(c(2, 2, -2, -2), 6)
# Offset original order by adding 
pc_byte_index <- dec_byte_index + byte_adjust
# Apply PC byte order to data
pc_bytes <- dec_bytes[pc_byte_index]
# Now the data can by read in the correct order and correction applied
pc_float <- readBin(pc_bytes, double(), n=6, size=4)
pc_float 
#> pc_float 
#[1]      1     12    123   1234  12345 123456

# Approach 2, use single index, reshape to matrix and apply 
# index representing desired order of 4 original bytes
byte_index <- c(3, 4, 1, 2)
# Convert data to matrix 
dec_byte_matrix <- matrix(dec_bytes, nrow=4, ncol=6)
# Use indicies to swap
pc_bytes <- dec_byte_matrix[index, ]
# Now compute floats
pc_float <- readBin(pc_bytes, double(), n=6, size=4)
#> pc_float 
#[1]      1     12    123   1234  12345 123456

我用microbench测试了一下，这两个之间的处理时间没有明显的区别。注意，对于原始DEC数据，pc_float需要除以4以获得正确答案，除非进行字节调整。