Different chemistry of batteries in operation
If you just take generic off the shelf converters and hook them up that way they will likely feed into each other and cook each other.  You can put diodes on their outputs so they can't back feed each other, but you lose some voltage in the diode and output voltage will vary a bit with current.  Even if you do this, they only correct for voltage at their output and one will inevitably maintain a slightly higher output voltage than the other.  This will tend to cause it to take almost all the load until it can no longer sustain its output at which point the other converter's voltage will be higher and it will take all the load.  It might not rapidly burn out if both converters are sized to support the full load, but it's not an ideal situation.
Paralleling power converters isn't particularly easy unless they are designed to work in parallel.  The higher the power the bigger the challenge.  If you're actually designing the converters yourself, you have to make them communicate with each other to balance load.  If you're good enough to do that, you can probably handle the additional challenge of doing it with two different input voltages.  Doing it with a high capacity or high power system, especially with Lithium ion Cells, or simply ensuring isolation and other factors will make the device fail safe for a commercial product is probably in the domain of engineers.  There is not necessarily an intrinsic loss of efficiency, just a big engineering challenge.
For a hobby version you weren't going to sell, you could probably do it with two relatively responsive isolated voltage converters and a microcontroller monitoring output voltage and current on both converters.  Challenge is increasing load on one converter while decreasing it on the other when both have different input voltage and duty cycle without too much effect on output voltafge, possibly while load is changing.  For a hobby version you could probably avoid the insane math skills needed by writing a program to experimentally determine values for a look up table and interpolating between values on the lookup table to correct imbalances.  If you have a lot of advanced math and Calculus skill, doing things the other way may look less intimidating for you than me.
As some other notes, the system would have to monitor both input battery voltages to ensure proper operation if one drops out and ensure low voltage cut off.  Because you'd need a microcontroller to begin with and you have the processing power available, it would probably be wise to build it to allow non-50/50 load balancing as well.