A CR2 is 15mm diameter by 27 mm long; a double long would by 15mm by 54mm - not a standard size, and you would need one with a 6V output.
There is a "15270" Li-Ion battery in the same size as a CR2. Newer Li-Ion batteries are rated at the same 3.0V output voltage as Li cells, and some 15270's are sold as "rechargeable CR2 batteries".
There are companies that will make you up a 15x54mm 6V Li-Ion battery pack if you really truly want one, but it will: (1) cost a whole lot more than two bog standard "Li-Ion CR2's"; (2) not fit any commercially available charger. Li-Ion cells can not be charged in a series configuration without special monitoring terminals - charging Li-Ion cells without monitoring can lead to jetting flames from the batteries. Lithium isn't happy when it is let out to play with the other elements.
Li-Ion cells have quite a few dissadvantages at the consumer level. They loose power just sitting around and are in constant need of recharging. Keeping them at-the-ready in an unsophisticated charger really eats into their life. In comparison, non-rechargeable Li cells keep their power for 10 years or more (I have some that are going strong after 30 years [though in applications that take only a breath of power]). There are lots and lots of different Li-Ion chemistries available and some are better or worse than others for self-discharge, charge-cycle lifetimes, internal resistance, discharge profile, etc., etc.. Unless you are dealing directly with the battery maker as an OEM it is difficult to know just what sort of Li-Ion battery you are buying. No-name ebay Chinese batteries may be very good or they may be factory rejects sold by a recycling firm. (*)
Amperage considerations aren't a big concern in a photographic application. Expect the motor to run slower and the flash to take longer to charge as the batteries age, that's about it.
That isn't to say there may not be problems. There are some CR123-sized Li batteries that are meant for non-photographic applications - they are considerably cheaper but they can't run a camera because the internal resistance is too high. It is always a good idea to check that the battery is sold for "photographic applications" [or lacking that, for "toys and games"].
Well designed equipment that uses batteries will take most any power you throw at it and not get damaged. It has to, as users will shove most anything that fits [and a whole lot that doesn't] into that ole' battery hole.
(*) I am presently using a lot of 'recycled' Chinese factory waste, paying $2 for an RF power connector rather than $45. For breadboarding 6KV RF power electronics [AKA basement pyrotechnics] who really cares what the gold plating on the (soon to be melted) connectors looks like.