Can you restate the two conditions? I am not certain what you are comparing.
First of all, you cannot run cables to both inputs at the same time on the sub. You could damage it and/or your preamp/processor. When you use the LFE input you are using the crossover in your processor. Therefore it will be controlled by the processor. The line in on the sub uses the sub's internal crossover and volume control. This in addition to having both inputs on the sub connected at the same time is why there is a difference in sound. Connecting both inputs on the sub at the same time can make one preamp try to drive the other. If you want to have both inputs connected at the same time. you need an A/B swtich.
It depends on input sensitivity and system calabration.
LFE sends seperate lower bass info than that of your fronts especially if system is setup for LFE. You can send more than 1 input to most subs. It is what input has more information and intensity as to how loud that you will hear. It is normal for LFE to be louder than front speaker.