The latest v2.0 alpha builds have support for eac3to.
Downloads : https://ci.appveyor.com/project/wieslawsoltes/batchencoder/build/artifacts
Any comments and suggestion regarding presets or command-line parameters are welcome 
AC3 format and presets:
<?xml version="1.0" encoding="UTF-8"?>
<Format id="EAC3TO_AC3" name="AC3 (ATSC A/52) - eac3to" template="$EXE $INFILE $OUTFILE -progressnumbers $OPTIONS" input="false" output="false" function="GetProgress_Eac3toEnc.progress" path="eac3to/eac3to.exe" success="0" type="0" formats="RAW,LPCM,PCM,WAV,W64,RF64,AC3,EAC3,DTS,DTSES,DTS9624,DTSHDHR,DTSHDMA,MLP,THD,THDAC3,FLAC,AAC" extension="AC3" default="3">
<Presets>
<Preset name="192 kbit/s" options="-192"/>
<Preset name="224 kbit/s" options="-224"/>
<Preset name="384 kbit/s" options="-384"/>
<Preset name="448 kbit/s" options="-448"/>
<Preset name="640 kbit/s" options="-640"/>
<Preset name="Extract the AC3 core of a TrueHD track" options="-core"/>
</Presets>
</Format>
DTS format and presets:
<?xml version="1.0" encoding="UTF-8"?>
<Format id="EAC3TO_DTS" name="DTS (Coherent Acoustics codec) - eac3to" template="$EXE $INFILE $OUTFILE -progressnumbers $OPTIONS" input="false" output="false" function="GetProgress_Eac3toEnc.progress" path="eac3to/eac3to.exe" success="0" type="0" formats="RAW,LPCM,PCM,WAV,W64,RF64,AC3,EAC3,DTS,DTSES,DTS9624,DTSHDHR,DTSHDMA,MLP,THD,THDAC3,FLAC,AAC" extension="DTS" default="0">
<Presets>
<Preset name="768 kbit/s" options="-768"/>
<Preset name="1536 kbit/s" options="-1536"/>
<Preset name="Extract the DTS core of a DTS-HD track" options="-core"/>
</Presets>
</Format>
Progress function in Lua:
function GetProgress(s)
if string.match(s, '^Done.%s-') ~= nil then return "100";
else return string.match(s, 'process: (%d+)%%'); end;
end