I don't know of a way to make that automatically happen, but I do know of a way to make it happen manually. Here is the code from my server.cfg for map rotation and changing. Admins can change to maps using the vstr (/amvstr for Reloaded) without disrupting the regular map rotation. I cut it down a bit as I have a lot more entries than this including custom maps, but you get the idea. If an admin wants to change to hoth siege, all they need to do is log in as an admin and type "/amvstr s_hoth" to set up the server for siege mode with custom settings, change the map to siege_hoth, and set the next map back to a map alias in the regular rotation.
What would be awesome is to have custom map voting for non-admins so that you could vote for maps and their settings based on these aliases and not break a custom rotation, but that would take a mod.
Code:
set g_allowvote "0"
set g_autoMapCycle "0"
// Map Rotation
set m1 "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf1; set nextmap vstr m2"
set m2 "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf2; set nextmap vstr m3"
set m3 "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf3; set nextmap vstr m4"
set m4 "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf4; set nextmap vstr m5"
set m5 "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf5; set nextmap vstr m1"
vstr m1
// Team Death Match
set t_vjun "set g_privateDuel 1; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 20; set bot_enable 1; set bot_minplayers 8; set g_gametype 6; map mp/ffa1; set nextmap vstr m1"
set t_tomb "set g_privateDuel 1; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 20; set bot_enable 1; set bot_minplayers 8; set g_gametype 6; map mp/ffa2; set nextmap vstr m2"
// Capture the Flag
set c_imperial "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf1; set nextmap vstr m1"
set c_hoth "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 1; set bot_minplayers 8; set g_gametype 8; map mp/ctf2; set nextmap vstr m2"
// Siege
set s_desert "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 0; set bot_minplayers 0; set g_gametype 7; map mp/siege_desert; set nextmap vstr m1"
set s_hoth "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 0; set bot_minplayers 0; set g_gametype 7; map mp/siege_hoth; set nextmap vstr m2"
set s_korriban "set g_privateDuel 0; set g_forcePowerDisable 0; set fraglimit 0; set timelimit 30; set bot_enable 0; set bot_minplayers 0; set g_gametype 7; map mp/siege_korriban; set nextmap vstr m3"
// Duel
set d_bespin "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 3; map mp/duel1; set nextmap vstr m1"
set d_generator "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 3; map mp/duel2; set nextmap vstr m2"
set d_shaft "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 3; map mp/duel3; set nextmap vstr m3"
// Power Duel
set p_bespin "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 4; map mp/duel1; set nextmap vstr m1"
set p_generator "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 4; map mp/duel2; set nextmap vstr m2"
set p_shaft "set g_privateDuel 1; set g_forcePowerDisable 32737; set fraglimit 1; set timelimit 0; set bot_enable 0; set bot_minplayers 0; set g_gametype 4; map mp/duel3; set nextmap vstr m3"