The compatible frameworks version is set differently depending on which version of Mage is used. I am not aware of any versions of mage that set the target version to 4.5. Mage is not a complete tool and there are various changes that Microsoft recommend that you perform manually using a text editor. I am using Powershell to edit my manifests after creating them with mage. You could probably manually change the targetVersion attribute to 4.5 and then re-sign the manifest.
Mage 3.5.30729.1
C:\Program Files (x86)\Microsoft SDKs\Windows\v10.0A\bin\NETFX 4.6.1 Tools\mage.exe
No compatibleFrameworks element in file
Mage 4.0.30319.18020
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0A\bin\NETFX 4.0 Tools\mage.exe
<compatibleFrameworks xmlns="urn:schemas-microsoft-com:clickonce.v2">
<framework targetVersion="4.0" profile="Client" supportedRuntime="4.0.30319" />
<framework targetVersion="4.0" profile="Full" supportedRuntime="4.0.30319" />
</compatibleFrameworks>
Mage 4.0.30319.33440
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.1A\bin\NETFX 4.5.1 Tools\mage.exe
<compatibleFrameworks xmlns="urn:schemas-microsoft-com:clickonce.v2">
<framework targetVersion="4.0" profile="Client" supportedRuntime="4.0.30319" />
<framework targetVersion="4.0" profile="Full" supportedRuntime="4.0.30319" />
</compatibleFrameworks>
Mage 4.6.81.0
C:\Program Files (x86)\Microsoft SDKs\Windows\v10.0A\bin\NETFX 4.6 Tools\mage.exe
<compatibleFrameworks xmlns="urn:schemas-microsoft-com:clickonce.v2">
<framework targetVersion="4.6" profile="Client" supportedRuntime="4.0.30319" />
<framework targetVersion="4.6" profile="Full" supportedRuntime="4.0.30319" />
</compatibleFrameworks>
Mage 4.6.1055.0
C:\Program Files (x86)\Microsoft SDKs\Windows\v10.0A\bin\NETFX 4.6.1 Tools\mage.exe
<compatibleFrameworks xmlns="urn:schemas-microsoft-com:clickonce.v2">
<framework targetVersion="4.6" profile="Client" supportedRuntime="4.0.30319" />
<framework targetVersion="4.6" profile="Full" supportedRuntime="4.0.30319" />
</compatibleFrameworks>
C:\Program Files\Microsoft SDKs\Windows\v8.0A\bin\NETFX 4.0 Tools\MAGE.exe
generates this OK... – Vojtěch Dohnal