Custom MTD overrides the values of the partition layout. You can flash any Hboot sizes from alpharev, but if recovery is patched with specific custom values, it is these that will be in use. You could flash any hboot partition at all and it would make no difference. So you have to reflash recovery to leave custom MTD as there is no unpatch.
Theres just one patch zip which reads the values in your mtdpartmap.txt. So you put your custom values in, patch recovery and reboot recovery. Then if you wish to change sizes, repeat that (not forgetting to restore nandroid and patch boot too.