In actuality, these were 'Disciplinary Regiments' vice penal units. There were two types of disciplinary units in the French army of the period: punishment (penal) units, which, depending on the level of crime those in them were guilty of, had varying degrees of severity; and rehabilitation units for apprehended draft dodgers. The Disciplinary Regiments were of the latter type. They received only 'the better class' of refractaires. Those apprehended that had criminal records went either to the colonial battalions or foreign battalions. The penal units were in a class by themselves and were actually used for pioneer work. You might want to check Chapter XXI of Swords Around A Throne for information in that regard.
The four Disciplinary Regiments had four battalions each. There were originally four of them: Mediterranean (based on Corsica), Walcheren, Ile-de-Re, and Belle-Isle. Later, a fifth, entitled 2d Mediterranean, was formed from the overflow from 1st Mediterranean. The cadres for these units were carefully chosen, many coming from the Imperial Guard. Officers and NCOs assigned to Mediterranean had to be able to speak Italian; those going to Walcheren, German or Dutch. Walcheren also contained a battalion of former Spanish prisoners of war, cadred by 'sure' Spanish officers and NCOs. They seem to have served loyally and ably. Their mission was to create 'good and willing' soldiers from them and they were remarkably successful. Eugene remarked on their reliability in 1811. They were first used as replacement depots, processing men who were sent to infantry, artillery, and engineer units. Some of their battalions were also used as 'carrier units' taking replacements forward to the field armies, the cadre returning to the depots.
When made into a 'combat worthy' infantry division in 1812 (the 35th), their commander was General Joseph Durerre. There were three battalions from Belle-Isle, Ile-de-Re, and Walcheren, and 2d Mediterranean as well as two from 1st Mediterranean. Unfortunately, I haven't found information on elite companies.
Later, the 1st Mediterranean was redesignated the 35th Legere, Belle-Isle the 36th Legere, Walcheren the 131st Ligne, Ile-de-Re the 132d Ligne, and 2d Mediterranean the 133d Ligne. I would assume that elite companies would be formed after the units had proven themselves under fire, which was Napoleon's usual policy, as he believed it took more than a tall man to make a grenadier. Under that assumption, the battalions probably had six companies of fusiliers initially, forming their two elite companies from picked men after their first action. With the hand-picked cadremen, that process would have been done somewhat quickly I would think.