LSTM for text with different sentences size, but same input-output sizes
The problem is, the LSTM results, after excluding the tags that correspond to the padding portion give outputs of different size than the input.

How do you get the "LSTM results"? Are the "LSTM results" extracted making a prediction for each word in the original sentence? 

The LSTM is not a problem to do what you want to do. It might be an issue of your implementation. If you put a snippet of code maybe you could get some help.