gdalwarp DEM with different resolution extents

I’m trying to convert DEM source (LIDAR is original source, in ASC format) to a custom internal format that has specific resolution and alignment values. I also want to generate different output resolutions (each lower resolution is 1/9th resolution of higher res).

I’ve written a GDAL plugin to convert from source DEM to the internal format, but it requires the source data to already be in the correct resolution and alignment. So I’m trying to figure out the right combination of gdalwarp, gdal_translate and gdal_retile to achieve this. I need the pixel spacing (resolution) to match the target format resolution and I need those pixels to align with the target formats restrictions. I’m fine cutting data off the edges of the source.

I use python to calculate the correct commands and run them. I end up with (target SRS is WGS84/EGM96 – hopefully I got the t_srs right).

gdalwarp -t_srs "+proj=longlat +datum=WGS84 +no_defs +geoidgrids=./egm96_15.gtx" -tap -et 0 -r bilinear -tr <res> <res> -te <res_xmin> <res_ymin> <res_xmax> <res_ymax> <src.vrt> <dest.tif>

where <res> is specific to the resolution (such as 0.00001028806584362140 for 1/27th AS). The -te values are specific to the alignment requirements for that specific resolution. So I figure out the coordinates of the target format file that is "inside" the source data (cutting off the edge), and make sure the extent is a multiple of the target file size (again staying inside the bounds of the source data).

Then I use gdal_retile to split up <dest.tif> into individual files to fit what my custom format needs (300×300, 1 pixel overlap, so I do 301×301).

Finally I use gdal_translate with my custom plugin to convert the split files to my custom format.

This seems to work for my different output resolutions, but when I try and view the data, the higher res data does not line up with the lower res data – when I load the higher res data over the top of the higher res data, terrain features do not line up as expected.

So first question: when gdalwarp process -te does it try and fit the source data to that extent (i.e. ‘squashing’ the source data to fit, assuming -te is smaller than source extent), or does it ‘cut off’ the part of the source data that is outside that extent? I’m trying to get it to cut it off. If it’s ‘squashing’ instead, that might be why I’m seeing alignment problems.
[edit : comment indicates that gdalwarp "cuts" the data]

I’ve also tried:

gdalwarp -t_srs "..." -tr <res> <res> <src.vrt> <temp.tif>
gdal_translate <res_xoff> <res_yoff> <res_xsize> <res_ysize> <temp.tif> <dest.tif>

i.e. just have gdalwap reproject without trying to "trim" or "align" the output, then use gdal_translate to do the trimming to match my desired alignment. But this seems to end up with the same problem, and I’m concerned that the pixel alignment won’t match up.

Does this sound like I’m going about this the right way? Any suggestions to try and figure how to re-project and trim the data to match resolution and alignment restrictions?

Thanks!