You could update the OutputName of your .wixproj and use an MSBuild variable to pass through the version number or any other variable you like.
My build script looks like this:
set PRODUCTVERSION=7.1.0.1
MSBuild.exe /p:Configuration=Debug /p:ProductVersion=%PRODUCTVERSION% Installer.wixproj
And my WiX project looks like this:
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">x86</Platform>
<ProductVersion>1.0.0.0</ProductVersion>
<ProjectGuid>{b7415c44-8d59-4ac2-b698-03e399a305e3}</ProjectGuid>
<SchemaVersion>2.0</SchemaVersion>
<OutputName>Installer.$(ProductVersion)</OutputName>
...
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x86' ">
<OutputPath>bin\$(Configuration)\</OutputPath>
<IntermediateOutputPath>obj\$(Configuration)\</IntermediateOutputPath>
<DefineConstants>Debug</DefineConstants>
<WixVariables>ProductVersion=$(ProductVersion)</WixVariables>
</PropertyGroup>
...
</Project>
The output would be:
Installer.7.1.0.1.msi